#Starting miRDeep2 /home/shared/mirdeep2/bin/miRDeep2.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.1-Peve-sRNAseq-miRdeep2-31bp-fastp-merged-cnidarian_miRBase/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/11.1-Peve-sRNAseq-miRdeep2-31bp-fastp-merged-cnidarian_miRBase/Peve-mirdeep2-mapping.arf none /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/cnidarian-mirbase-mature-v22.1-no_spaces.fa none -t S.purpuratus -P -v -g -1 miRDeep2 started at 15:10:16 mkdir mirdeep_runs/run_22_04_2024_t_15_10_16 #testing input files started: 15:10:38 sanity_check_mature_ref.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/cnidarian-mirbase-mature-v22.1-no_spaces.fa ended: 15:10:38 total:0h:0m:0s sanity_check_reads_ready_file.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.1-Peve-sRNAseq-miRdeep2-31bp-fastp-merged-cnidarian_miRBase/collapsed-reads-over17bp-mirdeep2.fasta started: 15:10:38 ended: 15:10:57 total:0h:0m:19s started: 15:10:57 sanity_check_genome.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/data/Porites_evermanni_v1_genomic-no_spaces.fna ended: 15:11:02 total:0h:0m:5s started: 15:11:02 sanity_check_mapping_file.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.1-Peve-sRNAseq-miRdeep2-31bp-fastp-merged-cnidarian_miRBase/Peve-mirdeep2-mapping.arf ended: 15:11:06 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/cnidarian-mirbase-mature-v22.1-no_spaces.fa > mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/cnidarian-mirbase-mature-v22.1-no_spaces.fa ended: 15:11:06 total:0h:0m:4s #parsing genome mappings parse_mappings.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.1-Peve-sRNAseq-miRdeep2-31bp-fastp-merged-cnidarian_miRBase/Peve-mirdeep2-mapping.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/mapping.arf_parsed.arf started: 15:11:06 ended: 15:11:33 total:0h:0m:27s #excising precursors started: 15:11:33 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_22_04_2024_t_15_10_16/tmp/mapping.arf_parsed.arf mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.fa mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.coords -1 1 801134 ended: 15:12:44 total:0h:1m:11s #preparing signature prepare_signature.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/E-Peve/output/11.1-Peve-sRNAseq-miRdeep2-31bp-fastp-merged-cnidarian_miRBase/collapsed-reads-over17bp-mirdeep2.fasta mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.fa 1 -o mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/signature.arf 2>>error_22_04_2024_t_15_10_16.log started: 15:12:44 ended: 15:16:41 total:0h:3m:57s #folding precursors started: 15:16:41 RNAfold < mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.fa -noPS > mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.str ended: 17:25:35 total:2h:8m:54s #computing randfold p-values select_for_randfold.pl mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/signature.arf mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.str > mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors_for_randfold.ids started: 17:25:35 ended: 17:28:02 total:0h:2m:27s started: 17:28:02 fastaselect.pl mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.fa mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors_for_randfold.ids > mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors_for_randfold.fa ended: 17:28:03 total:0h:0m:1s started: 17:28:03 randfold -s mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors_for_randfold.rand ended: 13:13:08 total:19h:45m:5s #running miRDeep core algorithm started: 13:13:15 miRDeep2_core_algorithm.pl mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/signature.arf mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.str -s mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/cnidarian-mirbase-mature-v22.1-no_spaces.fa -v -50 -l 15 -y mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors_for_randfold.rand > mirdeep_runs/run_22_04_2024_t_15_10_16/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 6969151. 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 7367105. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7370015. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7373824. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7456994. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7478797. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7542369. ended: 13:15:59 total:0h:2m:44s #running permuted controls started: 13:15:59 echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/signature.arf mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.str -s mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/cnidarian-mirbase-mature-v22.1-no_spaces.fa -v -50 -y mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors_for_randfold.rand > mirdeep_runs/run_22_04_2024_t_15_10_16/output.mrd' > mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/command_line perform_controls.pl mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/command_line mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.str 100 -a > mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/output_permuted.mrd 2>>error_22_04_2024_t_15_10_16.log ended: 19:58:47 total:6h:42m:48s #doing survey of accuracy survey.pl mirdeep_runs/run_22_04_2024_t_15_10_16/output.mrd -a mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/output_permuted.mrd -d 1 > mirdeep_runs/run_22_04_2024_t_15_10_16/survey.csv started: 19:58:47 ended: 20:0:25 total:0h:1m:38s #producing graphic results started: 20:0:25 make_html.pl -f mirdeep_runs/run_22_04_2024_t_15_10_16/output.mrd -p mirdeep_runs/run_22_04_2024_t_15_10_16/tmp/precursors.coords -v 0 -s mirdeep_runs/run_22_04_2024_t_15_10_16/survey.csv -c -e -r /home/shared/mirdeep2/bin//../Rfam_for_miRDeep.fa -y 22_04_2024_t_15_10_16 -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: 139209 # reads with at least one reported alignment: 769 (0.55%) # reads that failed to align: 138440 (99.45%) Reported 2392 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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