#Starting miRDeep2 /home/shared/mirdeep2/bin/miRDeep2.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed_reads_gt17bp_mirdeep2.fasta /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic-no_spaces.fna /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/Apul-mirdeep2-mapping.arf none /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/cnidarian-mirbase-mature-v22.1-no_spaces.fa none -t S.purpuratus -P -v -g -1 miRDeep2 started at 13:0:39 mkdir mirdeep_runs/run_03_04_2024_t_13_00_39 #testing input files started: 13:0:58 sanity_check_mature_ref.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/cnidarian-mirbase-mature-v22.1-no_spaces.fa ended: 13:0:58 total:0h:0m:0s sanity_check_reads_ready_file.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed_reads_gt17bp_mirdeep2.fasta started: 13:0:58 ended: 13:1:51 total:0h:0m:53s started: 13:1:51 sanity_check_genome.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic-no_spaces.fna ended: 13:1:54 total:0h:0m:3s started: 13:1:54 sanity_check_mapping_file.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/Apul-mirdeep2-mapping.arf ended: 13:2:03 total:0h:0m:9s Pre-quantitation is skipped caused by missing file with known precursor miRNAs rna2dna.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/cnidarian-mirbase-mature-v22.1-no_spaces.fa > mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/cnidarian-mirbase-mature-v22.1-no_spaces.fa ended: 13:2:03 total:0h:0m:9s #parsing genome mappings parse_mappings.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/Apul-mirdeep2-mapping.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/mapping.arf_parsed.arf started: 13:2:03 ended: 13:2:51 total:0h:0m:48s #excising precursors started: 13:2:51 excise_precursors_iterative_final.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic-no_spaces.fna mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/mapping.arf_parsed.arf mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.fa mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.coords -1 1 764114 ended: 13:3:46 total:0h:0m:55s #preparing signature prepare_signature.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed_reads_gt17bp_mirdeep2.fasta mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.fa 1 -o mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/signature.arf 2>>error_03_04_2024_t_13_00_39.log started: 13:3:46 ended: 13:10:32 total:0h:6m:46s #folding precursors started: 13:10:32 RNAfold < mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.fa -noPS > mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.str ended: 15:10:17 total:1h:59m:45s #computing randfold p-values select_for_randfold.pl mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/signature.arf mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.str > mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors_for_randfold.ids started: 15:10:17 ended: 15:13:14 total:0h:2m:57s started: 15:13:14 fastaselect.pl mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.fa mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors_for_randfold.ids > mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors_for_randfold.fa ended: 15:13:15 total:0h:0m:1s started: 15:13:15 randfold -s mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors_for_randfold.rand ended: 6:23:16 total:15h:10m:1s #running miRDeep core algorithm started: 6:23:24 miRDeep2_core_algorithm.pl mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/signature.arf mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.str -s mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/cnidarian-mirbase-mature-v22.1-no_spaces.fa -v -50 -l 16 -y mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors_for_randfold.rand > mirdeep_runs/run_03_04_2024_t_13_00_39/output.mrd Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 1740298. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 3140264. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 3140327. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 11666278. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 14930809. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 15059882. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 15059903. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 15705963. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 15943015. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16101854. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16186518. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16238851. ended: 6:26:29 total:0h:3m:5s #running permuted controls started: 6:26:29 echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/signature.arf mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.str -s mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/cnidarian-mirbase-mature-v22.1-no_spaces.fa -v -50 -y mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors_for_randfold.rand > mirdeep_runs/run_03_04_2024_t_13_00_39/output.mrd' > mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/command_line perform_controls.pl mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/command_line mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.str 100 -a > mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/output_permuted.mrd 2>>error_03_04_2024_t_13_00_39.log ended: 12:28:03 total:6h:1m:34s #doing survey of accuracy survey.pl mirdeep_runs/run_03_04_2024_t_13_00_39/output.mrd -a mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/output_permuted.mrd -d 1 > mirdeep_runs/run_03_04_2024_t_13_00_39/survey.csv started: 12:28:03 ended: 12:28:30 total:0h:0m:27s #producing graphic results started: 12:28:30 make_html.pl -f mirdeep_runs/run_03_04_2024_t_13_00_39/output.mrd -p mirdeep_runs/run_03_04_2024_t_13_00_39/tmp/precursors.coords -v 0 -s mirdeep_runs/run_03_04_2024_t_13_00_39/survey.csv -c -e -r /home/shared/mirdeep2/bin//../Rfam_for_miRDeep.fa -y 03_04_2024_t_13_00_39 -o -t S.purpuratus -V 2.0.1.2 parsing input file finished checking Rfam for hits to precursors Build bowtie index of Rfam entries Mapping mature,star and loop sequences against index # reads processed: 90182 # reads with at least one reported alignment: 461 (0.51%) # reads that failed to align: 89721 (99.49%) Reported 1700 alignments creating PDF files creating pdf for NC_058066.1_Acropora_millepora_isolate_JS-1_chromosome_1_Amil_v2.1_whole_genome_shotgun_sequence_49320 finished creating pdf for 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NW_025322675.1_Acropora_millepora_isolate_JS-1_unplaced_genomic_scaffold_Amil_v2.1_Sc0000183_whole_genome_shotgun_sequence_646676 finished creating pdf for NC_058076.1_Acropora_millepora_isolate_JS-1_chromosome_11_Amil_v2.1_whole_genome_shotgun_sequence_418765 finished creating pdf for NC_058074.1_Acropora_millepora_isolate_JS-1_chromosome_9_Amil_v2.1_whole_genome_shotgun_sequence_374842 finished creating pdf for NC_058069.1_Acropora_millepora_isolate_JS-1_chromosome_4_Amil_v2.1_whole_genome_shotgun_sequence_179048 finished creating pdf for NW_025322628.1_Acropora_millepora_isolate_JS-1_unplaced_genomic_scaffold_Amil_v2.1_Sc0000086_whole_genome_shotgun_sequence_593057 finished creating pdf for NC_058066.1_Acropora_millepora_isolate_JS-1_chromosome_1_Amil_v2.1_whole_genome_shotgun_sequence_50395 finished ended: 12:37:09 total:0h:8m:39s fasta and bed files have been created in subfolder mirna_results_03_04_2024_t_13_00_39 rmtree(mirdeep_runs/run_03_04_2024_t_13_00_39/tmp) miRDeep runtime: started: 13:0:39 ended: 12:37:10 total:23h:36m:31s