#Starting miRDeep2 /home/shared/mirdeep2/bin/miRDeep2.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.2-Peve-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed-reads-over17bp-mirdeep2.fasta /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/data/Porites_evermanni_v1_genomic-no_spaces.fna /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.2-Peve-sRNAseq-miRdeep2-31bp-fastp-merged/Peve-mirdeep2-mapping.arf none /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa none -t S.purpuratus -P -v -g -1 miRDeep2 started at 15:47:40 mkdir mirdeep_runs/run_15_04_2024_t_15_47_40 #testing input files started: 15:48:01 sanity_check_mature_ref.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa ended: 15:48:01 total:0h:0m:0s sanity_check_reads_ready_file.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.2-Peve-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed-reads-over17bp-mirdeep2.fasta started: 15:48:01 ended: 15:48:20 total:0h:0m:19s started: 15:48:20 sanity_check_genome.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/data/Porites_evermanni_v1_genomic-no_spaces.fna ended: 15:48:24 total:0h:0m:4s started: 15:48:24 sanity_check_mapping_file.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.2-Peve-sRNAseq-miRdeep2-31bp-fastp-merged/Peve-mirdeep2-mapping.arf ended: 15:48:28 total:0h:0m:4s Pre-quantitation is skipped caused by missing file with known precursor miRNAs rna2dna.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa > mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/mirbase-mature-v22.1-no_spaces.fa ended: 15:48:28 total:0h:0m:4s #parsing genome mappings parse_mappings.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.2-Peve-sRNAseq-miRdeep2-31bp-fastp-merged/Peve-mirdeep2-mapping.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/mapping.arf_parsed.arf started: 15:48:28 ended: 15:48:54 total:0h:0m:26s #excising precursors started: 15:48:54 excise_precursors_iterative_final.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/data/Porites_evermanni_v1_genomic-no_spaces.fna mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/mapping.arf_parsed.arf mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.fa mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.coords -1 1 801134 ended: 15:50:01 total:0h:1m:7s #preparing signature prepare_signature.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.2-Peve-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed-reads-over17bp-mirdeep2.fasta mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.fa 1 -o mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/signature.arf 2>>error_15_04_2024_t_15_47_40.log started: 15:50:01 ended: 15:53:36 total:0h:3m:35s #folding precursors started: 15:53:36 RNAfold < mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.fa -noPS > mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.str ended: 17:54:40 total:2h:1m:4s #computing randfold p-values select_for_randfold.pl mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/signature.arf mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.str > mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors_for_randfold.ids started: 17:54:40 ended: 17:57:02 total:0h:2m:22s started: 17:57:02 fastaselect.pl mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.fa mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors_for_randfold.ids > mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors_for_randfold.fa ended: 17:57:03 total:0h:0m:1s started: 17:57:03 randfold -s mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors_for_randfold.rand ended: 12:43:03 total:18h:46m:0s #running miRDeep core algorithm started: 12:43:06 miRDeep2_core_algorithm.pl mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/signature.arf mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.str -s mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/mirbase-mature-v22.1-no_spaces.fa -v -50 -l 15 -y mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors_for_randfold.rand > mirdeep_runs/run_15_04_2024_t_15_47_40/output.mrd Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 2731762. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 4806616. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 4806710. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 4949245. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 5359882. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 5425758. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 5673924. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6299056. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 6327441. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6464601. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 6536815. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6610410. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6936630. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7099308. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7222484. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7222486. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7222488. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7237954. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7312671. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7362843. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7362845. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7367105. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7457138. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7457140. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7534866. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7541135. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7542367. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7547147. ended: 12:45:42 total:0h:2m:36s #running permuted controls started: 12:45:42 echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/signature.arf mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.str -s mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/mirbase-mature-v22.1-no_spaces.fa -v -50 -y mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors_for_randfold.rand > mirdeep_runs/run_15_04_2024_t_15_47_40/output.mrd' > mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/command_line perform_controls.pl mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/command_line mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.str 100 -a > mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/output_permuted.mrd 2>>error_15_04_2024_t_15_47_40.log ended: 19:9:09 total:6h:23m:27s #doing survey of accuracy survey.pl mirdeep_runs/run_15_04_2024_t_15_47_40/output.mrd -a mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/output_permuted.mrd -d 1 > mirdeep_runs/run_15_04_2024_t_15_47_40/survey.csv started: 19:9:09 ended: 19:11:29 total:0h:2m:20s #producing graphic results started: 19:11:29 make_html.pl -f mirdeep_runs/run_15_04_2024_t_15_47_40/output.mrd -p mirdeep_runs/run_15_04_2024_t_15_47_40/tmp/precursors.coords -v 0 -s mirdeep_runs/run_15_04_2024_t_15_47_40/survey.csv -c -e -r /home/shared/mirdeep2/bin//../Rfam_for_miRDeep.fa -y 15_04_2024_t_15_47_40 -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: 139391 # reads with at least one reported alignment: 766 (0.55%) # reads that failed to align: 138625 (99.45%) Reported 2390 alignments creating PDF files creating pdf for Porites_evermani_scaffold_1503_530575 finished creating pdf for Porites_evermani_scaffold_26_42156 finished creating pdf for 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