#Starting miRDeep2 /home/shared/mirdeep2/bin/miRDeep2.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11-Apul-sRNAseq-miRdeep2/collapsed-reads-all-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 /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11-Apul-sRNAseq-miRdeep2/Apul-mirdeep2-mapping.arf none /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa none -t S.purpuratus -P -v -g -1 miRDeep2 started at 14:47:36 mkdir mirdeep_runs/run_08_11_2023_t_14_47_36 #testing input files started: 14:47:57 sanity_check_mature_ref.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa ended: 14:47:58 total:0h:0m:1s sanity_check_reads_ready_file.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11-Apul-sRNAseq-miRdeep2/collapsed-reads-all-mirdeep2.fasta started: 14:47:58 ended: 14:49:21 total:0h:1m:23s started: 14:49:21 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: 14:49:24 total:0h:0m:3s started: 14:49:24 sanity_check_mapping_file.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11-Apul-sRNAseq-miRdeep2/Apul-mirdeep2-mapping.arf ended: 14:49:35 total:0h:0m:11s Pre-quantitation is skipped caused by missing file with known precursor miRNAs rna2dna.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa > mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/mirbase-mature-v22.1-no_spaces.fa ended: 14:49:35 total:0h:0m:11s #parsing genome mappings parse_mappings.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11-Apul-sRNAseq-miRdeep2/Apul-mirdeep2-mapping.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/mapping.arf_parsed.arf started: 14:49:35 ended: 14:50:57 total:0h:1m:22s #excising precursors started: 14:50:57 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_08_11_2023_t_14_47_36/tmp/mapping.arf_parsed.arf mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.fa mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.coords -1 1 2387348 ended: 14:57:06 total:0h:6m:9s #preparing signature prepare_signature.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11-Apul-sRNAseq-miRdeep2/collapsed-reads-all-mirdeep2.fasta mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.fa 1 -o mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/signature.arf 2>>error_08_11_2023_t_14_47_36.log started: 14:57:06 ended: 15:21:31 total:0h:24m:25s #folding precursors started: 15:21:31 RNAfold < mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.fa -noPS > mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.str ended: 22:1:24 total:6h:39m:53s #computing randfold p-values select_for_randfold.pl mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/signature.arf mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.str > mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors_for_randfold.ids started: 22:1:24 ended: 22:10:09 total:0h:8m:45s started: 22:10:09 fastaselect.pl mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.fa mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors_for_randfold.ids > mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors_for_randfold.fa ended: 22:10:12 total:0h:0m:3s started: 22:10:12 randfold -s mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors_for_randfold.rand ended: 21:34:56 total:47h:24m:44s #running miRDeep core algorithm started: 21:36:07 miRDeep2_core_algorithm.pl mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/signature.arf mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.str -s mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/mirbase-mature-v22.1-no_spaces.fa -v -50 -l 16 -y mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors_for_randfold.rand > mirdeep_runs/run_08_11_2023_t_14_47_36/output.mrd Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 1419471. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 1457771. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 1764975. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 3621228. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 3794166. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7442695. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7553413. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9081057. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9081278. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9081820. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 11952684. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 13585873. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 13585906. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 14661192. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16046601. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16097956. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 16393368. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 20442015. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 20716994. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 22462218. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 24483448. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 25291277. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 25529812. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 25529830. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 28211861. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 28697537. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 30325729. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 31835018. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 32826166. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 33681173. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 34229459. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 34281292. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 37975548. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 37975550. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 38762909. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 38762915. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 39400229. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 39496452. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 39516922. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 39522015. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40089467. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40177244. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40177246. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40202704. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40347351. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40642758. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40654423. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40654425. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40783290. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40893438. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 40972399. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41073092. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41074803. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41331961. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41430305. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41634459. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41646808. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41788503. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41843815. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41848133. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41959100. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41959668. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41966582. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41968657. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 41985028. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 41992996. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42064708. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42091311. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42109566. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42159734. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42191628. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42213356. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42226978. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42230701. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42251164. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42251166. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42260520. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42262284. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42267517. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42295506. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42370820. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42386897. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42456716. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42484360. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 42535279. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42538778. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42539793. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42593838. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42593841. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42596031. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42603057. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42665967. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 42693513. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1445, line 42703349. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42834128. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42855924. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42859438. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42894540. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42919261. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 42999512. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 43018512. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 43038827. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 43054911. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 43131815. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 43181889. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 43230809. ended: 21:45:07 total:0h:9m:0s #running permuted controls started: 21:45:07 echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/signature.arf mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.str -s mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/mirbase-mature-v22.1-no_spaces.fa -v -50 -y mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors_for_randfold.rand > mirdeep_runs/run_08_11_2023_t_14_47_36/output.mrd' > mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/command_line perform_controls.pl mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/command_line mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.str 100 -a > mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/output_permuted.mrd 2>>error_08_11_2023_t_14_47_36.log ended: 20:19:23 total:22h:34m:16s #doing survey of accuracy survey.pl mirdeep_runs/run_08_11_2023_t_14_47_36/output.mrd -a mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/output_permuted.mrd -d 1 > mirdeep_runs/run_08_11_2023_t_14_47_36/survey.csv started: 20:19:23 ended: 20:20:57 total:0h:1m:34s #producing graphic results started: 20:20:57 make_html.pl -f mirdeep_runs/run_08_11_2023_t_14_47_36/output.mrd -p mirdeep_runs/run_08_11_2023_t_14_47_36/tmp/precursors.coords -v 0 -s mirdeep_runs/run_08_11_2023_t_14_47_36/survey.csv -c -e -r /home/shared/mirdeep2/bin//../Rfam_for_miRDeep.fa -y 08_11_2023_t_14_47_36 -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: 244953 # reads with at least one reported alignment: 696 (0.28%) # reads that failed to align: 244257 (99.72%) Reported 2371 alignments creating PDF files creating pdf for NC_058075.1_Acropora_millepora_isolate_JS-1_chromosome_10_Amil_v2.1_whole_genome_shotgun_sequence_1178449 finished creating pdf for NC_058075.1_Acropora_millepora_isolate_JS-1_chromosome_10_Amil_v2.1_whole_genome_shotgun_sequence_1234230 finished creating pdf for NC_058075.1_Acropora_millepora_isolate_JS-1_chromosome_10_Amil_v2.1_whole_genome_shotgun_sequence_1231100 finished creating pdf for NC_058075.1_Acropora_millepora_isolate_JS-1_chromosome_10_Amil_v2.1_whole_genome_shotgun_sequence_1178451 finished creating pdf for NC_058066.1_Acropora_millepora_isolate_JS-1_chromosome_1_Amil_v2.1_whole_genome_shotgun_sequence_157850 finished creating pdf for NC_058077.1_Acropora_millepora_isolate_JS-1_chromosome_12_Amil_v2.1_whole_genome_shotgun_sequence_1444410 finished creating pdf for NC_058079.1_Acropora_millepora_isolate_JS-1_chromosome_14_Amil_v2.1_whole_genome_shotgun_sequence_1622729 finished creating pdf for NC_058079.1_Acropora_millepora_isolate_JS-1_chromosome_14_Amil_v2.1_whole_genome_shotgun_sequence_1622645 finished creating pdf for NC_058079.1_Acropora_millepora_isolate_JS-1_chromosome_14_Amil_v2.1_whole_genome_shotgun_sequence_1622619 finished creating pdf for NC_058079.1_Acropora_millepora_isolate_JS-1_chromosome_14_Amil_v2.1_whole_genome_shotgun_sequence_1622673 finished creating pdf for NC_058070.1_Acropora_millepora_isolate_JS-1_chromosome_5_Amil_v2.1_whole_genome_shotgun_sequence_645592 finished creating pdf for NC_058068.1_Acropora_millepora_isolate_JS-1_chromosome_3_Amil_v2.1_whole_genome_shotgun_sequence_388375 finished creating pdf for NC_058070.1_Acropora_millepora_isolate_JS-1_chromosome_5_Amil_v2.1_whole_genome_shotgun_sequence_722310 finished creating pdf for NC_058071.1_Acropora_millepora_isolate_JS-1_chromosome_6_Amil_v2.1_whole_genome_shotgun_sequence_792399 finished creating pdf for NC_058068.1_Acropora_millepora_isolate_JS-1_chromosome_3_Amil_v2.1_whole_genome_shotgun_sequence_388377 finished creating pdf for 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NC_058078.1_Acropora_millepora_isolate_JS-1_chromosome_13_Amil_v2.1_whole_genome_shotgun_sequence_1575101 finished creating pdf for NC_058077.1_Acropora_millepora_isolate_JS-1_chromosome_12_Amil_v2.1_whole_genome_shotgun_sequence_1471096 finished creating pdf for NC_058066.1_Acropora_millepora_isolate_JS-1_chromosome_1_Amil_v2.1_whole_genome_shotgun_sequence_161547 finished creating pdf for NC_058074.1_Acropora_millepora_isolate_JS-1_chromosome_9_Amil_v2.1_whole_genome_shotgun_sequence_1160861 finished creating pdf for NC_058066.1_Acropora_millepora_isolate_JS-1_chromosome_1_Amil_v2.1_whole_genome_shotgun_sequence_130758 finished creating pdf for NW_025322622.1_Acropora_millepora_isolate_JS-1_unplaced_genomic_scaffold_Amil_v2.1_Sc0000061_whole_genome_shotgun_sequence_1785742 finished creating pdf for NC_058072.1_Acropora_millepora_isolate_JS-1_chromosome_7_Amil_v2.1_whole_genome_shotgun_sequence_871381 finished creating pdf for 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NW_025322891.1_Acropora_millepora_isolate_JS-1_unplaced_genomic_scaffold_Amil_v2.1_xfSc0000241_whole_genome_shotgun_sequence_2235442 finished creating pdf for NC_058066.1_Acropora_millepora_isolate_JS-1_chromosome_1_Amil_v2.1_whole_genome_shotgun_sequence_31910 finished creating pdf for NC_058074.1_Acropora_millepora_isolate_JS-1_chromosome_9_Amil_v2.1_whole_genome_shotgun_sequence_1081669 finished creating pdf for NC_058068.1_Acropora_millepora_isolate_JS-1_chromosome_3_Amil_v2.1_whole_genome_shotgun_sequence_403893 finished ended: 21:33:32 total:1h:12m:35s fasta and bed files have been created in subfolder mirna_results_08_11_2023_t_14_47_36 rmtree(mirdeep_runs/run_08_11_2023_t_14_47_36/tmp) miRDeep runtime: started: 14:47:36 ended: 21:33:35 total:78h:45m:59s