ShortStack version 4.1.0 Beginning run Options: { 'adapter': None, 'align_only': False, 'autotrim': False, 'autotrim_key': 'TCGGACCAGGCTTCATTCCCC', 'bamfile': None, 'dicermax': 24, 'dicermin': 21, 'dn_mirna': True, 'genomefile': '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/data/Pocillopora_meandrina_HIv1.assembly.fa', 'known_miRNAs': '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/M-multi-species/data/cnidarian-mirbase-mature-v22.1.fasta', 'locifile': None, 'locus': None, 'make_bigwigs': False, 'mincov': 1, 'mmap': 'u', 'nohp': False, 'outdir': '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A4-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A5-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A6-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B11-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B12-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B8-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C7-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C8-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C9-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D11-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E10-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E11-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E12-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E4-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E6-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E8-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F5-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F9-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G11-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G12-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G4-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G6-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G7-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G8-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G9-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H10-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H4-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H5-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H9-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2A1-fastp-adapters-polyG-31bp-merged.fq.gz'# reads processed: 2116434 # reads with at least one alignment: 1410847 (66.66%) # reads that failed to align: 705587 (33.34%) Reported 5934353 alignments , '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2A2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2C3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/01.10-F-Ptua-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2G2-fastp-adapters-polyG-31bp-merged.fq.gz'], 'strand_cutoff': 0.8, 'threads': 40} Required executable RNAfold : /home/sam/programs/mambaforge/envs/ShortStack-4.1.0_env/bin/RNAfold Required executable strucVis : /home/sam/programs/mambaforge/envs/ShortStack-4.1.0_env/bin/strucVis Required executable bowtie : /home/sam/programs/mambaforge/envs/ShortStack-4.1.0_env/bin/bowtie Required executable bowtie-build : /home/sam/programs/mambaforge/envs/ShortStack-4.1.0_env/bin/bowtie-build Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack-4.1.0_env/bin/samtools Wed 30 Apr 2025 17:04:31 -0700 PDT Condensing reads Wed 30 Apr 2025 17:48:15 -0700 PDT Required bowtie indices not found. Building them ... Completed Beginning alignment phase Wed 30 Apr 2025 17:53:44 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1A3-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 3 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 784148 # reads with at least one alignment: 509827 (65.02%) # reads that failed to align: 274321 (34.98%) Reported 1108905 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 592899/2116434 (28.0%) reads: 3554886/17060944 (20.8%) Multi-mapped placed with guidance (P): sequences: 426552/2116434 (20.2%) reads: 5258505/17060944 (30.8%) Multi-mapped randomly placed (R): sequences: 331542/2116434 (15.7%) reads: 1960913/17060944 (11.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 59854/2116434 (2.8%) reads: 489192/17060944 (2.9%) Not mapped (no hits)(N): sequences: 705587/2116434 (33.3%) reads: 5797448/17060944 (34.0%) Wed 30 Apr 2025 17:55:56 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1A4-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1688192 # reads with at least one alignment: 1304315 (77.26%) # reads that failed to align: 383877 (22.74%) Reported 3005294 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 300108/784148 (38.3%) reads: 723842/7301532 (9.9%) Multi-mapped placed with guidance (P): sequences: 136105/784148 (17.4%) reads: 3879576/7301532 (53.1%) Multi-mapped randomly placed (R): sequences: 64623/784148 (8.2%) reads: 2055427/7301532 (28.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 8991/784148 (1.1%) reads: 41615/7301532 (0.6%) Not mapped (no hits)(N): sequences: 274321/784148 (35.0%) reads: 601072/7301532 (8.2%) Wed 30 Apr 2025 17:56:31 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1A5-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1399839 # reads with at least one alignment: 994836 (71.07%) # reads that failed to align: 405003 (28.93%) Reported 2617956 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 955846/1688192 (56.6%) reads: 1947656/11304754 (17.2%) Multi-mapped placed with guidance (P): sequences: 176910/1688192 (10.5%) reads: 4711706/11304754 (41.7%) Multi-mapped randomly placed (R): sequences: 137368/1688192 (8.1%) reads: 3186560/11304754 (28.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 34191/1688192 (2.0%) reads: 108758/11304754 (1.0%) Not mapped (no hits)(N): sequences: 383877/1688192 (22.7%) reads: 1350074/11304754 (11.9%) Wed 30 Apr 2025 17:57:38 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1A6-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 886874 # reads with at least one alignment: 317390 (35.79%) # reads that failed to align: 569484 (64.21%) Reported 1075413 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 630216/1399839 (45.0%) reads: 1386447/9632775 (14.4%) Multi-mapped placed with guidance (P): sequences: 198628/1399839 (14.2%) reads: 4043545/9632775 (42.0%) Multi-mapped randomly placed (R): sequences: 138817/1399839 (9.9%) reads: 1805291/9632775 (18.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 27175/1399839 (1.9%) reads: 158171/9632775 (1.6%) Not mapped (no hits)(N): sequences: 405003/1399839 (28.9%) reads: 2239321/9632775 (23.2%) Wed 30 Apr 2025 17:58:43 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1B11-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 905253 # reads with at least one alignment: 620341 (68.53%) # reads that failed to align: 284912 (31.47%) Reported 2698551 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 123421/886874 (13.9%) reads: 429363/4965937 (8.6%) Multi-mapped placed with guidance (P): sequences: 104547/886874 (11.8%) reads: 1333787/4965937 (26.9%) Multi-mapped randomly placed (R): sequences: 78610/886874 (8.9%) reads: 550463/4965937 (11.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 10812/886874 (1.2%) reads: 77492/4965937 (1.6%) Not mapped (no hits)(N): sequences: 569484/886874 (64.2%) reads: 2574832/4965937 (51.8%) Wed 30 Apr 2025 17:59:22 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1B12-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 663653 # reads with at least one alignment: 447522 (67.43%) # reads that failed to align: 216131 (32.57%) Reported 1446420 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 250189/905253 (27.6%) reads: 1405332/6957969 (20.2%) Multi-mapped placed with guidance (P): sequences: 169883/905253 (18.8%) reads: 2163487/6957969 (31.1%) Multi-mapped randomly placed (R): sequences: 168523/905253 (18.6%) reads: 834568/6957969 (12.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 31746/905253 (3.5%) reads: 173192/6957969 (2.5%) Not mapped (no hits)(N): sequences: 284912/905253 (31.5%) reads: 2381390/6957969 (34.2%) Wed 30 Apr 2025 18:00:29 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1B8-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1791641 # reads with at least one alignment: 1349931 (75.35%) # reads that failed to align: 441710 (24.65%) Reported 3048597 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 240326/663653 (36.2%) reads: 757157/5509163 (13.7%) Multi-mapped placed with guidance (P): sequences: 94352/663653 (14.2%) reads: 2046811/5509163 (37.2%) Multi-mapped randomly placed (R): sequences: 96127/663653 (14.5%) reads: 1493720/5509163 (27.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 16717/663653 (2.5%) reads: 68184/5509163 (1.2%) Not mapped (no hits)(N): sequences: 216131/663653 (32.6%) reads: 1143291/5509163 (20.8%) Wed 30 Apr 2025 18:01:07 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1C1-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1187952 # reads with at least one alignment: 631183 (53.13%) # reads that failed to align: 556769 (46.87%) Reported 1909190 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 997958/1791641 (55.7%) reads: 1834021/9730281 (18.8%) Multi-mapped placed with guidance (P): sequences: 184807/1791641 (10.3%) reads: 4018269/9730281 (41.3%) Multi-mapped randomly placed (R): sequences: 132146/1791641 (7.4%) reads: 2219852/9730281 (22.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 35020/1791641 (2.0%) reads: 101498/9730281 (1.0%) Not mapped (no hits)(N): sequences: 441710/1791641 (24.7%) reads: 1556641/9730281 (16.0%) Wed 30 Apr 2025 18:02:23 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1C2-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 805442 # reads with at least one alignment: 515503 (64.00%) # reads that failed to align: 289939 (36.00%) Reported 1796705 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 343515/1187952 (28.9%) reads: 973432/9136756 (10.7%) Multi-mapped placed with guidance (P): sequences: 148094/1187952 (12.5%) reads: 3790674/9136756 (41.5%) Multi-mapped randomly placed (R): sequences: 117578/1187952 (9.9%) reads: 2354662/9136756 (25.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 21996/1187952 (1.9%) reads: 91283/9136756 (1.0%) Not mapped (no hits)(N): sequences: 556769/1187952 (46.9%) reads: 1926705/9136756 (21.1%) Wed 30 Apr 2025 18:03:17 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1C3-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 832374 # reads with at least one alignment: 458888 (55.13%) # reads that failed to align: 373486 (44.87%) Reported 1659175 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 257654/805442 (32.0%) reads: 1307167/12142922 (10.8%) Multi-mapped placed with guidance (P): sequences: 117791/805442 (14.6%) reads: 3001776/12142922 (24.7%) Multi-mapped randomly placed (R): sequences: 120073/805442 (14.9%) reads: 1546733/12142922 (12.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 19985/805442 (2.5%) reads: 116753/12142922 (1.0%) Not mapped (no hits)(N): sequences: 289939/805442 (36.0%) reads: 6170493/12142922 (50.8%) Wed 30 Apr 2025 18:04:11 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1C7-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 482284 # reads with at least one alignment: 327768 (67.96%) # reads that failed to align: 154516 (32.04%) Reported 1097240 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 215686/832374 (25.9%) reads: 905363/7009289 (12.9%) Multi-mapped placed with guidance (P): sequences: 110645/832374 (13.3%) reads: 1945266/7009289 (27.8%) Multi-mapped randomly placed (R): sequences: 114746/832374 (13.8%) reads: 912842/7009289 (13.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 17811/832374 (2.1%) reads: 88014/7009289 (1.3%) Not mapped (no hits)(N): sequences: 373486/832374 (44.9%) reads: 3157804/7009289 (45.1%) Wed 30 Apr 2025 18:04:58 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1C8-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 727844 # reads with at least one alignment: 500054 (68.70%) # reads that failed to align: 227790 (31.30%) Reported 2057681 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 171337/482284 (35.5%) reads: 740612/6664480 (11.1%) Multi-mapped placed with guidance (P): sequences: 66679/482284 (13.8%) reads: 1561156/6664480 (23.4%) Multi-mapped randomly placed (R): sequences: 77274/482284 (16.0%) reads: 805861/6664480 (12.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 12478/482284 (2.6%) reads: 63206/6664480 (0.9%) Not mapped (no hits)(N): sequences: 154516/482284 (32.0%) reads: 3493645/6664480 (52.4%) Wed 30 Apr 2025 18:05:32 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1C9-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1323057 # reads with at least one alignment: 1026594 (77.59%) # reads that failed to align: 296463 (22.41%) Reported 2140688 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 219062/727844 (30.1%) reads: 1204063/7215955 (16.7%) Multi-mapped placed with guidance (P): sequences: 123822/727844 (17.0%) reads: 2070101/7215955 (28.7%) Multi-mapped randomly placed (R): sequences: 134422/727844 (18.5%) reads: 843427/7215955 (11.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 22748/727844 (3.1%) reads: 131163/7215955 (1.8%) Not mapped (no hits)(N): sequences: 227790/727844 (31.3%) reads: 2967201/7215955 (41.1%) Wed 30 Apr 2025 18:06:27 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1D11-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 801315 # reads with at least one alignment: 540378 (67.44%) # reads that failed to align: 260937 (32.56%) Reported 2455718 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 787603/1323057 (59.5%) reads: 1416013/7583706 (18.7%) Multi-mapped placed with guidance (P): sequences: 117034/1323057 (8.8%) reads: 3092592/7583706 (40.8%) Multi-mapped randomly placed (R): sequences: 98708/1323057 (7.5%) reads: 2382475/7583706 (31.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 23249/1323057 (1.8%) reads: 59622/7583706 (0.8%) Not mapped (no hits)(N): sequences: 296463/1323057 (22.4%) reads: 633004/7583706 (8.3%) Wed 30 Apr 2025 18:07:25 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1E10-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 986782 # reads with at least one alignment: 760929 (77.11%) # reads that failed to align: 225853 (22.89%) Reported 1646507 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 198255/801315 (24.7%) reads: 1455567/7499565 (19.4%) Multi-mapped placed with guidance (P): sequences: 156074/801315 (19.5%) reads: 2181511/7499565 (29.1%) Multi-mapped randomly placed (R): sequences: 159832/801315 (19.9%) reads: 825891/7499565 (11.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 26217/801315 (3.3%) reads: 169275/7499565 (2.3%) Not mapped (no hits)(N): sequences: 260937/801315 (32.6%) reads: 2867321/7499565 (38.2%) Wed 30 Apr 2025 18:08:16 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1E11-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 751751 # reads with at least one alignment: 540715 (71.93%) # reads that failed to align: 211036 (28.07%) Reported 1743997 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 567065/986782 (57.5%) reads: 1063328/5959777 (17.8%) Multi-mapped placed with guidance (P): sequences: 93538/986782 (9.5%) reads: 2541287/5959777 (42.6%) Multi-mapped randomly placed (R): sequences: 81670/986782 (8.3%) reads: 1873380/5959777 (31.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 18656/986782 (1.9%) reads: 49632/5959777 (0.8%) Not mapped (no hits)(N): sequences: 225853/986782 (22.9%) reads: 432150/5959777 (7.3%) Wed 30 Apr 2025 18:09:14 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1E12-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 760018 # reads with at least one alignment: 523392 (68.87%) # reads that failed to align: 236626 (31.13%) Reported 1954452 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 304862/751751 (40.6%) reads: 859538/6928895 (12.4%) Multi-mapped placed with guidance (P): sequences: 99215/751751 (13.2%) reads: 2965414/6928895 (42.8%) Multi-mapped randomly placed (R): sequences: 116628/751751 (15.5%) reads: 1762839/6928895 (25.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 20010/751751 (2.7%) reads: 75967/6928895 (1.1%) Not mapped (no hits)(N): sequences: 211036/751751 (28.1%) reads: 1265137/6928895 (18.3%) Wed 30 Apr 2025 18:10:17 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1E4-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 773637 # reads with at least one alignment: 517124 (66.84%) # reads that failed to align: 256513 (33.16%) Reported 1991252 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 250306/760018 (32.9%) reads: 1396009/11932359 (11.7%) Multi-mapped placed with guidance (P): sequences: 122356/760018 (16.1%) reads: 1765401/11932359 (14.8%) Multi-mapped randomly placed (R): sequences: 129356/760018 (17.0%) reads: 1269220/11932359 (10.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 21374/760018 (2.8%) reads: 112656/11932359 (0.9%) Not mapped (no hits)(N): sequences: 236626/760018 (31.1%) reads: 7389073/11932359 (61.9%) Wed 30 Apr 2025 18:11:16 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1E6-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 753839 # reads with at least one alignment: 542236 (71.93%) # reads that failed to align: 211603 (28.07%) Reported 1684075 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 237881/773637 (30.7%) reads: 1750278/12643564 (13.8%) Multi-mapped placed with guidance (P): sequences: 122010/773637 (15.8%) reads: 2750134/12643564 (21.8%) Multi-mapped randomly placed (R): sequences: 134485/773637 (17.4%) reads: 888965/12643564 (7.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 22748/773637 (2.9%) reads: 149862/12643564 (1.2%) Not mapped (no hits)(N): sequences: 256513/773637 (33.2%) reads: 7104325/12643564 (56.2%) Wed 30 Apr 2025 18:12:13 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1E8-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1023499 # reads with at least one alignment: 528521 (51.64%) # reads that failed to align: 494978 (48.36%) Reported 1860314 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 324452/753839 (43.0%) reads: 891040/7397619 (12.0%) Multi-mapped placed with guidance (P): sequences: 90073/753839 (11.9%) reads: 2366867/7397619 (32.0%) Multi-mapped randomly placed (R): sequences: 107522/753839 (14.3%) reads: 1507997/7397619 (20.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 20189/753839 (2.7%) reads: 70015/7397619 (0.9%) Not mapped (no hits)(N): sequences: 211603/753839 (28.1%) reads: 2561700/7397619 (34.6%) Wed 30 Apr 2025 18:13:09 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1F2-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1048848 # reads with at least one alignment: 668448 (63.73%) # reads that failed to align: 380400 (36.27%) Reported 2857471 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 229942/1023499 (22.5%) reads: 1057858/9560237 (11.1%) Multi-mapped placed with guidance (P): sequences: 152562/1023499 (14.9%) reads: 2184626/9560237 (22.9%) Multi-mapped randomly placed (R): sequences: 126818/1023499 (12.4%) reads: 1508781/9560237 (15.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 19199/1023499 (1.9%) reads: 132468/9560237 (1.4%) Not mapped (no hits)(N): sequences: 494978/1023499 (48.4%) reads: 4676504/9560237 (48.9%) Wed 30 Apr 2025 18:14:12 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1F5-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 886892 # reads with at least one alignment: 607228 (68.47%) # reads that failed to align: 279664 (31.53%) Reported 2174436 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 259295/1048848 (24.7%) reads: 1851191/11044886 (16.8%) Multi-mapped placed with guidance (P): sequences: 198508/1048848 (18.9%) reads: 2590185/11044886 (23.5%) Multi-mapped randomly placed (R): sequences: 181276/1048848 (17.3%) reads: 868213/11044886 (7.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 29369/1048848 (2.8%) reads: 211400/11044886 (1.9%) Not mapped (no hits)(N): sequences: 380400/1048848 (36.3%) reads: 5523897/11044886 (50.0%) Wed 30 Apr 2025 18:15:36 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1F9-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 773676 # reads with at least one alignment: 564030 (72.90%) # reads that failed to align: 209646 (27.10%) Reported 1522171 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 293708/886892 (33.1%) reads: 1209517/7114117 (17.0%) Multi-mapped placed with guidance (P): sequences: 151211/886892 (17.0%) reads: 2380488/7114117 (33.5%) Multi-mapped randomly placed (R): sequences: 138015/886892 (15.6%) reads: 1027743/7114117 (14.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 24294/886892 (2.7%) reads: 125961/7114117 (1.8%) Not mapped (no hits)(N): sequences: 279664/886892 (31.5%) reads: 2370408/7114117 (33.3%) Wed 30 Apr 2025 18:16:38 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1G11-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1144724 # reads with at least one alignment: 884495 (77.27%) # reads that failed to align: 260229 (22.73%) Reported 2025053 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 362802/773676 (46.9%) reads: 884677/5837855 (15.2%) Multi-mapped placed with guidance (P): sequences: 87512/773676 (11.3%) reads: 1872031/5837855 (32.1%) Multi-mapped randomly placed (R): sequences: 97263/773676 (12.6%) reads: 1847962/5837855 (31.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 16453/773676 (2.1%) reads: 61543/5837855 (1.1%) Not mapped (no hits)(N): sequences: 209646/773676 (27.1%) reads: 1171642/5837855 (20.1%) Wed 30 Apr 2025 18:17:29 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1G12-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 2850728 # reads with at least one alignment: 2270088 (79.63%) # reads that failed to align: 580640 (20.37%) Reported 4319800 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 642709/1144724 (56.1%) reads: 1148550/6074744 (18.9%) Multi-mapped placed with guidance (P): sequences: 118183/1144724 (10.3%) reads: 2451063/6074744 (40.3%) Multi-mapped randomly placed (R): sequences: 100211/1144724 (8.8%) reads: 1949873/6074744 (32.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 23392/1144724 (2.0%) reads: 55167/6074744 (0.9%) Not mapped (no hits)(N): sequences: 260229/1144724 (22.7%) reads: 470091/6074744 (7.7%) Wed 30 Apr 2025 18:18:39 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1G2-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 3 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1193619 # reads with at least one alignment: 832912 (69.78%) # reads that failed to align: 360707 (30.22%) Reported 2340095 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1824024/2850728 (64.0%) reads: 3236142/11999334 (27.0%) Multi-mapped placed with guidance (P): sequences: 253224/2850728 (8.9%) reads: 3850235/11999334 (32.1%) Multi-mapped randomly placed (R): sequences: 152376/2850728 (5.3%) reads: 3714954/11999334 (31.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 40464/2850728 (1.4%) reads: 146127/11999334 (1.2%) Not mapped (no hits)(N): sequences: 580640/2850728 (20.4%) reads: 1051876/11999334 (8.8%) Wed 30 Apr 2025 18:20:34 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1G4-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1323325 # reads with at least one alignment: 1003145 (75.80%) # reads that failed to align: 320180 (24.20%) Reported 2729036 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 527935/1193619 (44.2%) reads: 1251937/8636021 (14.5%) Multi-mapped placed with guidance (P): sequences: 140256/1193619 (11.8%) reads: 3263543/8636021 (37.8%) Multi-mapped randomly placed (R): sequences: 138288/1193619 (11.6%) reads: 1792504/8636021 (20.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 26433/1193619 (2.2%) reads: 98375/8636021 (1.1%) Not mapped (no hits)(N): sequences: 360707/1193619 (30.2%) reads: 2229662/8636021 (25.8%) Wed 30 Apr 2025 18:21:45 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1G6-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 865256 # reads with at least one alignment: 552084 (63.81%) # reads that failed to align: 313172 (36.19%) Reported 2348569 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 674687/1323325 (51.0%) reads: 1832854/12933178 (14.2%) Multi-mapped placed with guidance (P): sequences: 146705/1323325 (11.1%) reads: 4307648/12933178 (33.3%) Multi-mapped randomly placed (R): sequences: 149486/1323325 (11.3%) reads: 3997166/12933178 (30.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 32267/1323325 (2.4%) reads: 137238/12933178 (1.1%) Not mapped (no hits)(N): sequences: 320180/1323325 (24.2%) reads: 2658272/12933178 (20.6%) Wed 30 Apr 2025 18:23:05 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1G7-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 647270 # reads with at least one alignment: 381532 (58.94%) # reads that failed to align: 265738 (41.06%) Reported 1026361 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 203184/865256 (23.5%) reads: 1098680/7468017 (14.7%) Multi-mapped placed with guidance (P): sequences: 166341/865256 (19.2%) reads: 2203727/7468017 (29.5%) Multi-mapped randomly placed (R): sequences: 156606/865256 (18.1%) reads: 750117/7468017 (10.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 25953/865256 (3.0%) reads: 172076/7468017 (2.3%) Not mapped (no hits)(N): sequences: 313172/865256 (36.2%) reads: 3243417/7468017 (43.4%) Wed 30 Apr 2025 18:24:12 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1G8-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 885362 # reads with at least one alignment: 591892 (66.85%) # reads that failed to align: 293470 (33.15%) Reported 2464653 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 207964/647270 (32.1%) reads: 575452/7021160 (8.2%) Multi-mapped placed with guidance (P): sequences: 95270/647270 (14.7%) reads: 1724294/7021160 (24.6%) Multi-mapped randomly placed (R): sequences: 66382/647270 (10.3%) reads: 3775864/7021160 (53.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 11916/647270 (1.8%) reads: 57422/7021160 (0.8%) Not mapped (no hits)(N): sequences: 265738/647270 (41.1%) reads: 888128/7021160 (12.6%) Wed 30 Apr 2025 18:24:45 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1G9-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 923013 # reads with at least one alignment: 695578 (75.36%) # reads that failed to align: 227435 (24.64%) Reported 1825758 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 241648/885362 (27.3%) reads: 1247264/7120640 (17.5%) Multi-mapped placed with guidance (P): sequences: 165025/885362 (18.6%) reads: 1783256/7120640 (25.0%) Multi-mapped randomly placed (R): sequences: 161392/885362 (18.2%) reads: 1495790/7120640 (21.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 23827/885362 (2.7%) reads: 120085/7120640 (1.7%) Not mapped (no hits)(N): sequences: 293470/885362 (33.1%) reads: 2474245/7120640 (34.7%) Wed 30 Apr 2025 18:26:07 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1H10-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 845283 # reads with at least one alignment: 543540 (64.30%) # reads that failed to align: 301743 (35.70%) Reported 2189966 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 473923/923013 (51.3%) reads: 1014642/6232963 (16.3%) Multi-mapped placed with guidance (P): sequences: 96679/923013 (10.5%) reads: 2385692/6232963 (38.3%) Multi-mapped randomly placed (R): sequences: 103833/923013 (11.2%) reads: 1524827/6232963 (24.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 21143/923013 (2.3%) reads: 66424/6232963 (1.1%) Not mapped (no hits)(N): sequences: 227435/923013 (24.6%) reads: 1241378/6232963 (19.9%) Wed 30 Apr 2025 18:27:09 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1H4-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1449782 # reads with at least one alignment: 1079249 (74.44%) # reads that failed to align: 370533 (25.56%) Reported 2235878 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 226821/845283 (26.8%) reads: 1358251/10190960 (13.3%) Multi-mapped placed with guidance (P): sequences: 147850/845283 (17.5%) reads: 3234462/10190960 (31.7%) Multi-mapped randomly placed (R): sequences: 144443/845283 (17.1%) reads: 1041976/10190960 (10.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 24426/845283 (2.9%) reads: 179074/10190960 (1.8%) Not mapped (no hits)(N): sequences: 301743/845283 (35.7%) reads: 4377197/10190960 (43.0%) Wed 30 Apr 2025 18:28:11 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1H5-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 531861 # reads with at least one alignment: 380268 (71.50%) # reads that failed to align: 151593 (28.50%) Reported 981255 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 820077/1449782 (56.6%) reads: 1419449/9255506 (15.3%) Multi-mapped placed with guidance (P): sequences: 134599/1449782 (9.3%) reads: 3610126/9255506 (39.0%) Multi-mapped randomly placed (R): sequences: 100903/1449782 (7.0%) reads: 3480790/9255506 (37.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 23670/1449782 (1.6%) reads: 55601/9255506 (0.6%) Not mapped (no hits)(N): sequences: 370533/1449782 (25.6%) reads: 689540/9255506 (7.5%) Wed 30 Apr 2025 18:29:21 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/1H9-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1120704 # reads with at least one alignment: 860149 (76.75%) # reads that failed to align: 260555 (23.25%) Reported 1903951 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 239524/531861 (45.0%) reads: 616573/8040284 (7.7%) Multi-mapped placed with guidance (P): sequences: 66253/531861 (12.5%) reads: 2694323/8040284 (33.5%) Multi-mapped randomly placed (R): sequences: 62991/531861 (11.8%) reads: 4165579/8040284 (51.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 11500/531861 (2.2%) reads: 38271/8040284 (0.5%) Not mapped (no hits)(N): sequences: 151593/531861 (28.5%) reads: 525538/8040284 (6.5%) Wed 30 Apr 2025 18:29:57 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/2A1-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 798679 # reads with at least one alignment: 547425 (68.54%) # reads that failed to align: 251254 (31.46%) Reported 1888495 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 651293/1120704 (58.1%) reads: 1381264/8096143 (17.1%) Multi-mapped placed with guidance (P): sequences: 89474/1120704 (8.0%) reads: 2826149/8096143 (34.9%) Multi-mapped randomly placed (R): sequences: 97968/1120704 (8.7%) reads: 2448528/8096143 (30.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 21414/1120704 (1.9%) reads: 54577/8096143 (0.7%) Not mapped (no hits)(N): sequences: 260555/1120704 (23.2%) reads: 1385625/8096143 (17.1%) Wed 30 Apr 2025 18:31:01 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/2A2-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 1 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1452146 # reads with at least one alignment: 1093929 (75.33%) # reads that failed to align: 358217 (24.67%) Reported 2747928 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 282475/798679 (35.4%) reads: 1205219/9913617 (12.2%) Multi-mapped placed with guidance (P): sequences: 113314/798679 (14.2%) reads: 3157741/9913617 (31.9%) Multi-mapped randomly placed (R): sequences: 130111/798679 (16.3%) reads: 1037909/9913617 (10.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 21525/798679 (2.7%) reads: 143022/9913617 (1.4%) Not mapped (no hits)(N): sequences: 251254/798679 (31.5%) reads: 4369726/9913617 (44.1%) Wed 30 Apr 2025 18:31:34 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/2C3-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 1281373 # reads with at least one alignment: 934255 (72.91%) # reads that failed to align: 347118 (27.09%) Reported 3489310 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 762234/1452146 (52.5%) reads: 1923113/13950879 (13.8%) Multi-mapped placed with guidance (P): sequences: 153675/1452146 (10.6%) reads: 4808660/13950879 (34.5%) Multi-mapped randomly placed (R): sequences: 148711/1452146 (10.2%) reads: 3728126/13950879 (26.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 29309/1452146 (2.0%) reads: 131200/13950879 (0.9%) Not mapped (no hits)(N): sequences: 358217/1452146 (24.7%) reads: 3359780/13950879 (24.1%) Wed 30 Apr 2025 18:32:10 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/2G2-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 2 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... Converting to sorted bam format Uniquely mapped (U): sequences: 448380/1281373 (35.0%) reads: 1537180/10811663 (14.2%) Multi-mapped placed with guidance (P): sequences: 237596/1281373 (18.5%) reads: 4413834/10811663 (40.8%) Multi-mapped randomly placed (R): sequences: 207492/1281373 (16.2%) reads: 3232546/10811663 (29.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 40787/1281373 (3.2%) reads: 168709/10811663 (1.6%) Not mapped (no hits)(N): sequences: 347118/1281373 (27.1%) reads: 1459394/10811663 (13.5%) Wed 30 Apr 2025 18:33:30 -0700 PDT Merging and indexing alignments Wed 30 Apr 2025 18:37:10 -0700 PDT Defining small RNA clusters de novo With 345880446 total reads and mincov of 1 reads per million, the min read depth is 346 Wed 30 Apr 2025 18:37:59 -0700 PDT Analyzing cluster properties using 40 threads # reads processed: 49415 # reads with at least one alignment: 171 (0.35%) # reads that failed to align: 49244 (99.65%) Reported 1856 alignments [bam_sort_core] merging from 0 files and 40 in-memory blocks... Wed 30 Apr 2025 18:39:09 -0700 PDT Completed Wed 30 Apr 2025 18:39:09 -0700 PDT Searching for valid microRNA loci Aligning known_miRNAs sequences to genome Screening of possible microRNAs from user provided known_miRNAs Screening of possible de novo microRNAs Wed 30 Apr 2025 18:39:44 -0700 PDT Analyzing cluster properties using 40 threads Wed 30 Apr 2025 18:39:45 -0700 PDT Completed Writing final files Found a total of 40 MIRNA loci Non-MIRNA loci by DicerCall: N 7126 23 19 22 16 21 13 24 7 Creating visualizations of microRNA loci with strucVis <<< WARNING >>> Do not rely on these results alone to annotate new MIRNA loci! The false positive rate for de novo MIRNA identification is low, but NOT ZERO Insepct each mirna locus, especially the strucVis output, and see https://doi.org/10.1105/tpc.17.00851 , https://doi.org/10.1093/nar/gky1141 Wed 30 Apr 2025 18:39:57 -0700 PDT Run Completed! real 95m29.261s user 579m43.123s sys 230m2.435s