#Starting miRDeep2 /home/shared/mirdeep2/bin/miRDeep2.pl 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 Apul-mirdeep2-mapping.arf none /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/cnidarian_miRNAs.fasta none -P -v -g -1 miRDeep2 started at 11:15:00 mkdir mirdeep_runs/run_16_05_2024_t_11_15_00 #testing input files started: 11:15:20 sanity_check_mature_ref.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/cnidarian_miRNAs.fasta ended: 11:15:20 total:0h:0m:0s sanity_check_reads_ready_file.pl collapsed_reads_gt17bp_mirdeep2.fasta started: 11:15:20 ended: 11:16:16 total:0h:0m:56s started: 11:16:16 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: 11:16:19 total:0h:0m:3s started: 11:16:19 sanity_check_mapping_file.pl Apul-mirdeep2-mapping.arf ended: 11:16:29 total:0h:0m:10s 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_miRNAs.fasta > mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/cnidarian_miRNAs.fasta ended: 11:16:29 total:0h:0m:10s #parsing genome mappings parse_mappings.pl Apul-mirdeep2-mapping.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/mapping.arf_parsed.arf started: 11:16:29 ended: 11:17:18 total:0h:0m:49s #excising precursors started: 11:17:18 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_16_05_2024_t_11_15_00/tmp/mapping.arf_parsed.arf mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.fa mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.coords -1 1 764114 ended: 11:18:15 total:0h:0m:57s #preparing signature prepare_signature.pl collapsed_reads_gt17bp_mirdeep2.fasta mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.fa 1 -o mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/signature.arf 2>>error_16_05_2024_t_11_15_00.log started: 11:18:15 ended: 11:25:25 total:0h:7m:10s #folding precursors started: 11:25:25 RNAfold < mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.fa -noPS > mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.str ended: 13:28:44 total:2h:3m:19s #computing randfold p-values select_for_randfold.pl mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/signature.arf mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.str > mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors_for_randfold.ids started: 13:28:44 ended: 13:32:03 total:0h:3m:19s started: 13:32:03 fastaselect.pl mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.fa mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors_for_randfold.ids > mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors_for_randfold.fa ended: 13:32:04 total:0h:0m:1s started: 13:32:04 randfold -s mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors_for_randfold.rand ended: 4:57:16 total:15h:25m:12s #running miRDeep core algorithm started: 4:57:34 miRDeep2_core_algorithm.pl mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/signature.arf mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.str -s mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/cnidarian_miRNAs.fasta -v -50 -l 21 -y mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors_for_randfold.rand > mirdeep_runs/run_16_05_2024_t_11_15_00/output.mrd Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 1731351. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 3134971. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 3135031. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 11743978. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 14829084. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 14829105. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 15043106. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 15431758. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 15811473. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 15960835. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16153483. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16177236. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16177238. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16195008. ended: 5:0:39 total:0h:3m:5s #running permuted controls started: 5:0:39 echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/signature.arf mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.str -s mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/cnidarian_miRNAs.fasta -v -50 -y mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors_for_randfold.rand > mirdeep_runs/run_16_05_2024_t_11_15_00/output.mrd' > mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/command_line perform_controls.pl mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/command_line mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.str 100 -a > mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/output_permuted.mrd 2>>error_16_05_2024_t_11_15_00.log ended: 11:0:48 total:6h:0m:9s #doing survey of accuracy survey.pl mirdeep_runs/run_16_05_2024_t_11_15_00/output.mrd -a mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/output_permuted.mrd -d 1 > mirdeep_runs/run_16_05_2024_t_11_15_00/survey.csv started: 11:0:48 ended: 11:1:13 total:0h:0m:25s #producing graphic results started: 11:1:13 make_html.pl -f mirdeep_runs/run_16_05_2024_t_11_15_00/output.mrd -p mirdeep_runs/run_16_05_2024_t_11_15_00/tmp/precursors.coords -v 0 -s mirdeep_runs/run_16_05_2024_t_11_15_00/survey.csv -c -e -r /home/shared/mirdeep2/bin//../Rfam_for_miRDeep.fa -y 16_05_2024_t_11_15_00 -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 # reads processed: 90131 # reads with at least one reported alignment: 457 (0.51%) # reads that failed to align: 89674 (99.49%) Reported 1677 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 NC_058070.1_Acropora_millepora_isolate_JS-1_chromosome_5_Amil_v2.1_whole_genome_shotgun_sequence_208678 finished creating pdf for NC_058068.1_Acropora_millepora_isolate_JS-1_chromosome_3_Amil_v2.1_whole_genome_shotgun_sequence_123927 finished creating pdf for NC_058071.1_Acropora_millepora_isolate_JS-1_chromosome_6_Amil_v2.1_whole_genome_shotgun_sequence_256047 finished creating pdf 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subfolder mirna_results_16_05_2024_t_11_15_00 rmtree(mirdeep_runs/run_16_05_2024_t_11_15_00/tmp) miRDeep runtime: started: 11:15:00 ended: 11:5:35 total:23h:50m:35s