#Starting miRDeep2 /home/shared/mirdeep2/bin/miRDeep2.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/11.2-Pmea-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed-reads-over17bp-mirdeep2.fasta /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/data/Pmea/Pocillopora_meandrina_HIv1_nospaces.assembly.fasta /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/11.2-Pmea-sRNAseq-miRdeep2-31bp-fastp-merged/Pmea-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 9:48:38 mkdir mirdeep_runs/run_19_04_2024_t_09_48_38 #testing input files started: 9:49:03 sanity_check_mature_ref.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1-no_spaces.fa ended: 9:49:03 total:0h:0m:0s sanity_check_reads_ready_file.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/11.2-Pmea-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed-reads-over17bp-mirdeep2.fasta started: 9:49:03 ended: 9:49:41 total:0h:0m:38s started: 9:49:41 sanity_check_genome.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/data/Pmea/Pocillopora_meandrina_HIv1_nospaces.assembly.fasta ended: 9:49:42 total:0h:0m:1s started: 9:49:42 sanity_check_mapping_file.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/11.2-Pmea-sRNAseq-miRdeep2-31bp-fastp-merged/Pmea-mirdeep2-mapping.arf ended: 9:49:47 total:0h:0m:5s 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_19_04_2024_t_09_48_38/tmp/mirbase-mature-v22.1-no_spaces.fa ended: 9:49:47 total:0h:0m:5s #parsing genome mappings parse_mappings.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/11.2-Pmea-sRNAseq-miRdeep2-31bp-fastp-merged/Pmea-mirdeep2-mapping.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/mapping.arf_parsed.arf started: 9:49:47 ended: 9:50:20 total:0h:0m:33s #excising precursors started: 9:50:20 excise_precursors_iterative_final.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/data/Pmea/Pocillopora_meandrina_HIv1_nospaces.assembly.fasta mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/mapping.arf_parsed.arf mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.fa mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.coords -1 1 995574 ended: 9:51:43 total:0h:1m:23s #preparing signature prepare_signature.pl /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/11.2-Pmea-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed-reads-over17bp-mirdeep2.fasta mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.fa 1 -o mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/signature.arf 2>>error_19_04_2024_t_09_48_38.log started: 9:51:43 ended: 9:56:31 total:0h:4m:48s #folding precursors started: 9:56:31 RNAfold < mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.fa -noPS > mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.str ended: 12:31:53 total:2h:35m:22s #computing randfold p-values select_for_randfold.pl mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/signature.arf mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.str > mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors_for_randfold.ids started: 12:31:53 ended: 12:34:57 total:0h:3m:4s started: 12:34:57 fastaselect.pl mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.fa mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors_for_randfold.ids > mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors_for_randfold.fa ended: 12:34:58 total:0h:0m:1s started: 12:34:58 randfold -s mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors_for_randfold.rand ended: 16:11:41 total:27h:36m:43s #running miRDeep core algorithm started: 16:11:51 miRDeep2_core_algorithm.pl mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/signature.arf mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.str -s mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/mirbase-mature-v22.1-no_spaces.fa -v -50 -l 15 -y mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors_for_randfold.rand > mirdeep_runs/run_19_04_2024_t_09_48_38/output.mrd Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 2145246. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 4958890. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6028014. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6191822. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6191830. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6210358. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6591440. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 6920060. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7073161. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7370839. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7534951. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 7931145. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8570900. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8586297. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8631141. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8634912. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8634915. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8651517. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8669272. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8704845. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8797565. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8831795. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 8961653. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9015773. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9088759. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9129186. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9218613. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9333810. Negative repeat count does nothing at /home/shared/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1458, line 9359622. Unable to flush stdout: No space left on device ended: 16:15:04 total:0h:3m:13s #running permuted controls started: 16:15:04 echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/signature.arf mirdeep_runs/run_19_04_2024_t_09_48_38/tmp/precursors.st miRDeep runtime: started: 9:48:38 ended: 16:15:09 total: