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...

[Wed Nov 15 15:16:46 2023]
rule prepare_genome:
    input: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa
    output: data/genomes/Peve-MirMachine.fai, data/genomes/Peve-MirMachine.size
    jobid: 4
    reason: Missing output files: data/genomes/Peve-MirMachine.size
    resources: tmpdir=/tmp


[Wed Nov 15 15:16:46 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/Peve-MirMachine/Mir-7370.PRE.result
    jobid: 910
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-7370.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-7370.PRE
    threads: 15
    resources: tmpdir=/tmp


[Wed Nov 15 15:16:46 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/Peve-MirMachine/Mir-4766.PRE.result
    jobid: 636
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-4766.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-4766.PRE
    threads: 15
    resources: tmpdir=/tmp


[Wed Nov 15 15:16:46 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/Peve-MirMachine.mirna_nodes.csv
    jobid: 1673
    reason: Missing output files: analyses/search/Peve-MirMachine.mirna_nodes.csv
    wildcards: species=Peve-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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:16:48 2023]
Finished job 1673.
1 of 2231 steps (0.0%) done
Select jobs to execute...
[Wed Nov 15 15:16:48 2023]
Finished job 4.
2 of 2231 steps (0.1%) done
Removing temporary output data/genomes/Peve-MirMachine.fai.
[Wed Nov 15 15:16:52 2023]
Finished job 910.
3 of 2231 steps (0.1%) done

[Wed Nov 15 15:16:52 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-7370.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-7370.PRE.gff, analyses/output/Peve-MirMachine/Mir-7370.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-7370.PRE.unfiltered
    jobid: 909
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-7370.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-7370.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-7370.PRE
    resources: tmpdir=/tmp


[Wed Nov 15 15:16:52 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/Peve-MirMachine/Mir-974.PRE.result
    jobid: 1080
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-974.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-974.PRE
    threads: 15
    resources: tmpdir=/tmp

[Wed Nov 15 15:16:54 2023]
Finished job 636.
4 of 2231 steps (0.2%) done
Select jobs to execute...

[Wed Nov 15 15:16:54 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/Peve-MirMachine/Mir-3068.PRE.result
    jobid: 482
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-3068.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-3068.PRE
    threads: 15
    resources: tmpdir=/tmp


[Wed Nov 15 15:16:54 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-4766.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-4766.PRE.gff, analyses/output/Peve-MirMachine/Mir-4766.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-4766.PRE.unfiltered
    jobid: 635
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-4766.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-4766.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-4766.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:16:55 2023]
Finished job 909.
5 of 2231 steps (0.2%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-7370.PRE.ext.gff.
Select jobs to execute...

[Wed Nov 15 15:16:55 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-7370.PRE.filtered.gff
    jobid: 1569
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-7370.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-7370.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-7370.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:16:55 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-7370.PRE.filtered.fasta
    jobid: 2128
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-7370.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-7370.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-7370.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:16:55 2023]
Finished job 2128.
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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:16:55 2023]
Finished job 1569.
7 of 2231 steps (0.3%) done
[Wed Nov 15 15:16:57 2023]
Finished job 635.
8 of 2231 steps (0.4%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-4766.PRE.ext.gff.

[Wed Nov 15 15:16:57 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-4766.PRE.filtered.gff
    jobid: 1432
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-4766.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-4766.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-4766.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:16:57 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-4766.PRE.filtered.fasta
    jobid: 1991
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-4766.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-4766.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-4766.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:16:57 2023]
Finished job 1991.
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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:16:57 2023]
Finished job 1432.
10 of 2231 steps (0.4%) done
[Wed Nov 15 15:17:00 2023]
Finished job 482.
11 of 2231 steps (0.5%) done

[Wed Nov 15 15:17:00 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-3068.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-3068.PRE.gff, analyses/output/Peve-MirMachine/Mir-3068.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-3068.PRE.unfiltered
    jobid: 481
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-3068.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-3068.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-3068.PRE
    resources: tmpdir=/tmp


[Wed Nov 15 15:17:00 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/Peve-MirMachine/Mir-7180.PRE.result
    jobid: 842
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-7180.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-7180.PRE
    threads: 15
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:00 2023]
Finished job 481.
12 of 2231 steps (1%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-3068.PRE.ext.gff.
Select jobs to execute...

[Wed Nov 15 15:17:00 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-3068.PRE.filtered.gff
    jobid: 1355
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-3068.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-3068.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-3068.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:00 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-3068.PRE.filtered.fasta
    jobid: 1914
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-3068.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-3068.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-3068.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:00 2023]
Finished job 1914.
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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:17:00 2023]
Finished job 1355.
14 of 2231 steps (1%) done
[Wed Nov 15 15:17:06 2023]
Finished job 842.
15 of 2231 steps (1%) done

[Wed Nov 15 15:17:06 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-7180.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-7180.PRE.gff, analyses/output/Peve-MirMachine/Mir-7180.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-7180.PRE.unfiltered
    jobid: 841
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-7180.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-7180.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-7180.PRE
    resources: tmpdir=/tmp


[Wed Nov 15 15:17:06 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/Peve-MirMachine/Mir-4969.PRE.result
    jobid: 722
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-4969.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-4969.PRE
    threads: 15
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:06 2023]
Finished job 841.
16 of 2231 steps (1%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-7180.PRE.ext.gff.
Select jobs to execute...

[Wed Nov 15 15:17:07 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-7180.PRE.filtered.gff
    jobid: 1535
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-7180.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-7180.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-7180.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:07 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-7180.PRE.filtered.fasta
    jobid: 2094
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-7180.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-7180.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-7180.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:07 2023]
Finished job 2094.
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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:17:07 2023]
Finished job 1535.
18 of 2231 steps (1%) done
[Wed Nov 15 15:17:14 2023]
Finished job 1080.
19 of 2231 steps (1%) done

[Wed Nov 15 15:17:14 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/Peve-MirMachine/Mir-14.PRE.result
    jobid: 120
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-14.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-14.PRE
    threads: 15
    resources: tmpdir=/tmp


[Wed Nov 15 15:17:14 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-974.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-974.PRE.gff, analyses/output/Peve-MirMachine/Mir-974.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-974.PRE.unfiltered
    jobid: 1079
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-974.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-974.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-974.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:14 2023]
Finished job 1079.
20 of 2231 steps (1%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-974.PRE.ext.gff.
Select jobs to execute...

[Wed Nov 15 15:17:14 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-974.PRE.filtered.gff
    jobid: 1654
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-974.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-974.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-974.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:14 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-974.PRE.filtered.fasta
    jobid: 2213
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-974.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-974.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-974.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:14 2023]
Finished job 722.
21 of 2231 steps (1%) done
Select jobs to execute...

[Wed Nov 15 15:17:14 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-4969.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-4969.PRE.gff, analyses/output/Peve-MirMachine/Mir-4969.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-4969.PRE.unfiltered
    jobid: 721
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-4969.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-4969.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-4969.PRE
    resources: tmpdir=/tmp


[Wed Nov 15 15:17:14 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/Peve-MirMachine/Mir-223.PRE.result
    jobid: 362
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-223.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-223.PRE
    threads: 15
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:14 2023]
Finished job 2213.
22 of 2231 steps (1%) done
Select jobs to execute...
[Wed Nov 15 15:17:14 2023]
Finished job 721.
23 of 2231 steps (1%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-4969.PRE.ext.gff.

[Wed Nov 15 15:17:14 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-4969.PRE.filtered.gff
    jobid: 1475
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-4969.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-4969.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-4969.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:14 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-4969.PRE.filtered.fasta
    jobid: 2034
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-4969.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-4969.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-4969.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...
[Wed Nov 15 15:17:14 2023]
Finished job 2034.
24 of 2231 steps (1%) 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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:17:14 2023]
Finished job 1654.
25 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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:17:15 2023]
Finished job 1475.
26 of 2231 steps (1%) done
[Wed Nov 15 15:17:25 2023]
Finished job 120.
27 of 2231 steps (1%) done

[Wed Nov 15 15:17:25 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-14.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-14.PRE.gff, analyses/output/Peve-MirMachine/Mir-14.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-14.PRE.unfiltered
    jobid: 119
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-14.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-14.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-14.PRE
    resources: tmpdir=/tmp


[Wed Nov 15 15:17:25 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/Peve-MirMachine/Mir-2022.PRE.result
    jobid: 300
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-2022.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-2022.PRE
    threads: 15
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:25 2023]
Finished job 119.
28 of 2231 steps (1%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-14.PRE.ext.gff.
Select jobs to execute...

[Wed Nov 15 15:17:25 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-14.PRE.filtered.gff
    jobid: 1174
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-14.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-14.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-14.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:25 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-14.PRE.filtered.fasta
    jobid: 1733
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-14.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-14.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-14.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:25 2023]
Finished job 1733.
29 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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:17:26 2023]
Finished job 1174.
30 of 2231 steps (1%) done
[Wed Nov 15 15:17:27 2023]
Finished job 362.
31 of 2231 steps (1%) done

[Wed Nov 15 15:17:27 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-223.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-223.PRE.gff, analyses/output/Peve-MirMachine/Mir-223.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-223.PRE.unfiltered
    jobid: 361
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-223.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-223.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-223.PRE
    resources: tmpdir=/tmp


[Wed Nov 15 15:17:27 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/Peve-MirMachine/Mir-203.PRE.result
    jobid: 302
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-203.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-203.PRE
    threads: 15
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:27 2023]
Finished job 361.
32 of 2231 steps (1%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-223.PRE.ext.gff.
Select jobs to execute...

[Wed Nov 15 15:17:27 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-223.PRE.filtered.gff
    jobid: 1295
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-223.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-223.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-223.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:27 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-223.PRE.filtered.fasta
    jobid: 1854
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-223.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-223.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-223.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:27 2023]
Finished job 1854.
33 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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:17:28 2023]
Finished job 1295.
34 of 2231 steps (2%) done
[Wed Nov 15 15:17:36 2023]
Finished job 300.
35 of 2231 steps (2%) done

[Wed Nov 15 15:17:36 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/Peve-MirMachine/Mir-340.PRE.result
    jobid: 542
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-340.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-340.PRE
    threads: 15
    resources: tmpdir=/tmp


[Wed Nov 15 15:17:36 2023]
rule parse_output:
    input: analyses/output/Peve-MirMachine/Mir-2022.PRE.result, data/genomes/Peve-MirMachine.size
    output: analyses/output/Peve-MirMachine/Mir-2022.PRE.gff, analyses/output/Peve-MirMachine/Mir-2022.PRE.ext.gff, analyses/output/Peve-MirMachine/Mir-2022.PRE.unfiltered
    jobid: 299
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-2022.PRE.gff; Input files updated by another job: data/genomes/Peve-MirMachine.size, analyses/output/Peve-MirMachine/Mir-2022.PRE.result
    wildcards: species=Peve-MirMachine, mirna=Mir-2022.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:36 2023]
Finished job 299.
36 of 2231 steps (2%) done
Removing temporary output analyses/output/Peve-MirMachine/Mir-2022.PRE.ext.gff.
Select jobs to execute...

[Wed Nov 15 15:17:36 2023]
rule fastas:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-2022.PRE.filtered.fasta
    jobid: 1823
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-2022.PRE.filtered.fasta; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-2022.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-2022.PRE
    resources: tmpdir=/tmp


[Wed Nov 15 15:17:36 2023]
rule create_filtered_gffs:
    input: analyses/output/Peve-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/Peve-MirMachine/Mir-2022.PRE.filtered.gff
    jobid: 1264
    reason: Missing output files: analyses/output/Peve-MirMachine/Mir-2022.PRE.filtered.gff; Input files updated by another job: analyses/output/Peve-MirMachine/Mir-2022.PRE.gff
    wildcards: species=Peve-MirMachine, mirna=Mir-2022.PRE
    resources: tmpdir=/tmp

[Wed Nov 15 15:17:36 2023]
Finished job 1823.
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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']
[Wed Nov 15 15:17:36 2023]
Finished job 1264.
38 of 2231 steps (2%) done
Will exit after finishing currently running jobs (scheduler).
[Wed Nov 15 15:17:41 2023]
[Wed Nov 15 15:17:41 2023]
Error in rule search_CM:
    jobid: 542
    input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-340.PRE.CM
    output: analyses/output/Peve-MirMachine/Mir-340.PRE.result
    shell:
        
		cmsearch --cpu 15 /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-340.PRE.CM /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa > analyses/output/Peve-MirMachine/Mir-340.PRE.result

		
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Error in rule search_CM:
    jobid: 302
    input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-203.PRE.CM
    output: analyses/output/Peve-MirMachine/Mir-203.PRE.result
    shell:
        
		cmsearch --cpu 15 /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-203.PRE.CM /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa > analyses/output/Peve-MirMachine/Mir-203.PRE.result

		
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job search_CM since they might be corrupted:
analyses/output/Peve-MirMachine/Mir-340.PRE.result
Removing output files of failed job search_CM since they might be corrupted:
analyses/output/Peve-MirMachine/Mir-203.PRE.result
Will exit after finishing currently running jobs (scheduler).
Shutting down, this might take some time.
Complete log: .snakemake/log/2023-11-15T151645.017352.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/E-Peve/data/Porites_evermanni_v1.fa
# Species: Peve-MirMachine
# Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Peve-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1.fa --cpu 40 --add-all-nodes
# miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999']