#Starting miRDeep2 /home/shared/mirdeep2/bin/miRDeep2.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/sRNAseq/mirtrace.config.output/qc_passed_reads.all.collapsed/no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1.fasta /home/shared/8TB_HDD_01/sam/data/P_evermanni/genomes/Porites_evermanni_v1.fa 20230809-peve-miRNA-mirdeep2-no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1.fasta.arf none none none miRDeep2 started at 15:17:52 mkdir mirdeep_runs/run_09_08_2023_t_15_17_52 #testing input files sanity_check_reads_ready_file.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/sRNAseq/mirtrace.config.output/qc_passed_reads.all.collapsed/no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1.fasta started: 15:18:00 ended: 15:18:06 total:0h:0m:6s started: 15:18:06 sanity_check_genome.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/genomes/Porites_evermanni_v1.fa ended: 15:18:11 total:0h:0m:5s started: 15:18:11 sanity_check_mapping_file.pl 20230809-peve-miRNA-mirdeep2-no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1.fasta.arf ended: 15:18:13 total:0h:0m:2s Pre-quantitation is skipped caused by missing file with known precursor miRNAs #parsing genome mappings parse_mappings.pl 20230809-peve-miRNA-mirdeep2-no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1.fasta.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/TP2.flexbar_trim.20230621_1.fasta.arf_parsed.arf started: 15:18:13 ended: 15:18:20 total:0h:0m:7s #excising precursors started: 15:18:20 excise_precursors_iterative_final.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/genomes/Porites_evermanni_v1.fa mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/TP2.flexbar_trim.20230621_1.fasta.arf_parsed.arf mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.fa mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.coords 50000 1 234138 2 173584 3 131928 4 102068 5 80314 6 64306 7 52278 8 42460 ended: 15:18:44 total:0h:0m:24s #preparing signature prepare_signature.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/sRNAseq/mirtrace.config.output/qc_passed_reads.all.collapsed/no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1.fasta mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.fa 1 -o mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/signature.arf 2>>error_09_08_2023_t_15_17_52.log started: 15:18:44 ended: 15:19:12 total:0h:0m:28s #folding precursors started: 15:19:12 RNAfold < mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.fa -noPS > mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.str ended: 15:26:40 total:0h:7m:28s #computing randfold p-values select_for_randfold.pl mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/signature.arf mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.str > mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors_for_randfold.ids started: 15:26:40 ended: 15:26:52 total:0h:0m:12s started: 15:26:52 fastaselect.pl mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.fa mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors_for_randfold.ids > mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors_for_randfold.fa ended: 15:26:52 total:0h:0m:0s started: 15:26:52 randfold -s mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors_for_randfold.rand ended: 16:28:11 total:1h:1m:19s #running miRDeep core algorithm started: 16:28:11 miRDeep2_core_algorithm.pl mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/signature.arf mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.str -v -50 -l 15 -y mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors_for_randfold.rand > mirdeep_runs/run_09_08_2023_t_15_17_52/output.mrd ended: 16:28:22 total:0h:0m:11s #running permuted controls started: 16:28:22 echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/signature.arf mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.str -v -50 -y mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors_for_randfold.rand > mirdeep_runs/run_09_08_2023_t_15_17_52/output.mrd' > mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/command_line perform_controls.pl mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/command_line mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.str 100 -a > mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/output_permuted.mrd 2>>error_09_08_2023_t_15_17_52.log ended: 16:47:45 total:0h:19m:23s #doing survey of accuracy survey.pl mirdeep_runs/run_09_08_2023_t_15_17_52/output.mrd -a mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/output_permuted.mrd -d 8 > mirdeep_runs/run_09_08_2023_t_15_17_52/survey.csv started: 16:47:45 ended: 16:47:47 total:0h:0m:2s #producing graphic results started: 16:47:47 make_html.pl -f mirdeep_runs/run_09_08_2023_t_15_17_52/output.mrd -p mirdeep_runs/run_09_08_2023_t_15_17_52/tmp/precursors.coords -v 0 -s mirdeep_runs/run_09_08_2023_t_15_17_52/survey.csv -c -e -r /home/shared/mirdeep2/bin//../Rfam_for_miRDeep.fa -y 09_08_2023_t_15_17_52 -o -V 2.0.1.2 No organism specified by switch -t [organism] so UCSC browser BLAT will not be used. To get a list of possible species names type make_html.pl -u Specify organism Reads are coming from by -t [organism] to get links in html file parsing input file finished checking Rfam for hits to precursors Build bowtie index of Rfam entries Mapping mature,star and loop sequences against index /home/shared/mirdeep2/bin/bowtie:24: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses import imp # reads processed: 6283 # reads with at least one reported alignment: 33 (0.53%) # reads that failed to align: 6250 (99.47%) Reported 104 alignments to 1 output stream(s) creating PDF files creating pdf for Porites_evermani_scaffold_910_22234 finished creating pdf for Porites_evermani_scaffold_1503_28005 finished creating pdf for Porites_evermani_scaffold_910_22228 finished creating pdf for Porites_evermani_scaffold_253_10769 finished creating pdf for Porites_evermani_scaffold_26_2292 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