#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-82-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-82-S1-TP2.flexbar_trim.20230621_1.fasta.arf none none none miRDeep2 started at 6:23:41 mkdir mirdeep_runs/run_10_08_2023_t_06_23_41 #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-82-S1-TP2.flexbar_trim.20230621_1.fasta started: 6:23:53 ended: 6:24:03 total:0h:0m:10s started: 6:24:03 sanity_check_genome.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/genomes/Porites_evermanni_v1.fa ended: 6:24:07 total:0h:0m:4s started: 6:24:07 sanity_check_mapping_file.pl 20230809-peve-miRNA-mirdeep2-no_spaces-sRNA-POR-82-S1-TP2.flexbar_trim.20230621_1.fasta.arf ended: 6:24:10 total:0h:0m:3s 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-82-S1-TP2.flexbar_trim.20230621_1.fasta.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/TP2.flexbar_trim.20230621_1.fasta.arf_parsed.arf started: 6:24:10 ended: 6:24:25 total:0h:0m:15s #excising precursors started: 6:24:25 excise_precursors_iterative_final.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/genomes/Porites_evermanni_v1.fa mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/TP2.flexbar_trim.20230621_1.fasta.arf_parsed.arf mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.fa mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.coords 50000 1 476978 2 265526 3 152194 4 92014 5 59604 6 42062 ended: 6:24:59 total:0h:0m:34s #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-82-S1-TP2.flexbar_trim.20230621_1.fasta mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.fa 1 -o mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/signature.arf 2>>error_10_08_2023_t_06_23_41.log started: 6:24:59 ended: 6:25:35 total:0h:0m:36s #folding precursors started: 6:25:35 RNAfold < mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.fa -noPS > mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.str ended: 6:31:51 total:0h:6m:16s #computing randfold p-values select_for_randfold.pl mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/signature.arf mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.str > mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors_for_randfold.ids started: 6:31:51 ended: 6:32:05 total:0h:0m:14s started: 6:32:05 fastaselect.pl mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.fa mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors_for_randfold.ids > mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors_for_randfold.fa ended: 6:32:05 total:0h:0m:0s started: 6:32:05 randfold -s mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors_for_randfold.rand ended: 7:25:00 total:0h:52m:55s #running miRDeep core algorithm started: 7:25:01 miRDeep2_core_algorithm.pl mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/signature.arf mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.str -v -50 -l 15 -y mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors_for_randfold.rand > mirdeep_runs/run_10_08_2023_t_06_23_41/output.mrd ended: 7:25:16 total:0h:0m:15s #running permuted controls started: 7:25:16 echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/signature.arf mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.str -v -50 -y mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors_for_randfold.rand > mirdeep_runs/run_10_08_2023_t_06_23_41/output.mrd' > mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/command_line perform_controls.pl mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/command_line mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.str 100 -a > mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/output_permuted.mrd 2>>error_10_08_2023_t_06_23_41.log ended: 7:51:09 total:0h:25m:53s #doing survey of accuracy survey.pl mirdeep_runs/run_10_08_2023_t_06_23_41/output.mrd -a mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/output_permuted.mrd -d 6 > mirdeep_runs/run_10_08_2023_t_06_23_41/survey.csv started: 7:51:09 ended: 7:51:10 total:0h:0m:1s #producing graphic results started: 7:51:10 make_html.pl -f mirdeep_runs/run_10_08_2023_t_06_23_41/output.mrd -p mirdeep_runs/run_10_08_2023_t_06_23_41/tmp/precursors.coords -v 0 -s mirdeep_runs/run_10_08_2023_t_06_23_41/survey.csv -c -e -r /home/shared/mirdeep2/bin//../Rfam_for_miRDeep.fa -y 10_08_2023_t_06_23_41 -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: 3282 # reads with at least one reported alignment: 21 (0.64%) # reads that failed to align: 3261 (99.36%) Reported 53 alignments to 1 output stream(s) creating PDF files creating pdf for Porites_evermani_scaffold_1503_27893 finished creating pdf for Porites_evermani_scaffold_26_1940 finished creating pdf for Porites_evermani_scaffold_72_4318 finished creating pdf for Porites_evermani_scaffold_1503_27895 finished creating pdf for Porites_evermani_scaffold_594_17589 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