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/E-Peve/data/Porites_evermanni_v1.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/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A11-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A7-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B4-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B6-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B7-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C11-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C12-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C5-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C6-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D12-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D5-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D7-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E7-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F10-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F12-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F6-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F7-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G10-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2A3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2B1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2D1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2D3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2E1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2E3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2F2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2H1-fastp-adapters-polyG-31bp-merged.fq.gz', # reads processed: 570348 # reads with at least one alignment: 445147 (78.05%) # reads that failed to align: 125201 (21.95%) Reported 1370946 alignments '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/01.10-E-Peve-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2H2-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 19:39:07 -0700 PDT Condensing reads Wed 30 Apr 2025 20:16:34 -0700 PDT Required bowtie indices not found. Building them ... Completed Beginning alignment phase Wed 30 Apr 2025 20:28:46 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1A11-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: 1030164 # reads with at least one alignment: 647911 (62.89%) # reads that failed to align: 382253 (37.11%) Reported 1992495 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 235852/570348 (41.4%) reads: 838920/2615338 (32.1%) Multi-mapped placed with guidance (P): sequences: 80369/570348 (14.1%) reads: 394044/2615338 (15.1%) Multi-mapped randomly placed (R): sequences: 114849/570348 (20.1%) reads: 389770/2615338 (14.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 14077/570348 (2.5%) reads: 554000/2615338 (21.2%) Not mapped (no hits)(N): sequences: 125201/570348 (22.0%) reads: 438604/2615338 (16.8%) Wed 30 Apr 2025 20:29:25 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1A7-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: 2302 # reads with at least one alignment: 1478 (64.21%) # reads that failed to align: 824 (35.79%) Reported 4536 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 352946/1030164 (34.3%) reads: 1824093/8013945 (22.8%) Multi-mapped placed with guidance (P): sequences: 126840/1030164 (12.3%) reads: 755455/8013945 (9.4%) Multi-mapped randomly placed (R): sequences: 145398/1030164 (14.1%) reads: 626799/8013945 (7.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 22727/1030164 (2.2%) reads: 170246/8013945 (2.1%) Not mapped (no hits)(N): sequences: 382253/1030164 (37.1%) reads: 4637352/8013945 (57.9%) Wed 30 Apr 2025 20:30:26 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1B3-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 # reads processed: 3275111 # reads with at least one alignment: 1284284 (39.21%) # reads that failed to align: 1990827 (60.79%) Reported 3706424 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 841/2302 (36.5%) reads: 1897/5254 (36.1%) Multi-mapped placed with guidance (P): sequences: 49/2302 (2.1%) reads: 99/5254 (1.9%) Multi-mapped randomly placed (R): sequences: 533/2302 (23.2%) reads: 680/5254 (12.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 55/2302 (2.4%) reads: 83/5254 (1.6%) Not mapped (no hits)(N): sequences: 824/2302 (35.8%) reads: 2495/5254 (47.5%) Wed 30 Apr 2025 20:30:27 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1B4-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 4 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 401361 # reads with at least one alignment: 251441 (62.65%) # reads that failed to align: 149920 (37.35%) Reported 670960 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 701793/3275111 (21.4%) reads: 2551235/12038476 (21.2%) Multi-mapped placed with guidance (P): sequences: 287663/3275111 (8.8%) reads: 1391296/12038476 (11.6%) Multi-mapped randomly placed (R): sequences: 258953/3275111 (7.9%) reads: 993464/12038476 (8.3%) Very highly multi-mapped (>=20 hits)(H): sequences: 35875/3275111 (1.1%) reads: 405634/12038476 (3.4%) Not mapped (no hits)(N): sequences: 1990827/3275111 (60.8%) reads: 6696847/12038476 (55.6%) Wed 30 Apr 2025 20:32:09 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1B6-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: 20932 # reads with at least one alignment: 16005 (76.46%) # reads that failed to align: 4927 (23.54%) Reported 55464 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 150696/401361 (37.5%) reads: 527661/1334606 (39.5%) Multi-mapped placed with guidance (P): sequences: 35744/401361 (8.9%) reads: 149482/1334606 (11.2%) Multi-mapped randomly placed (R): sequences: 58141/401361 (14.5%) reads: 129300/1334606 (9.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 6860/401361 (1.7%) reads: 75491/1334606 (5.7%) Not mapped (no hits)(N): sequences: 149920/401361 (37.4%) reads: 452672/1334606 (33.9%) Wed 30 Apr 2025 20:32:21 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1B7-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: 239 # reads with at least one alignment: 125 (52.30%) # reads that failed to align: 114 (47.70%) Reported 419 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 8029/20932 (38.4%) reads: 23156/80353 (28.8%) Multi-mapped placed with guidance (P): sequences: 1319/20932 (6.3%) reads: 4488/80353 (5.6%) Multi-mapped randomly placed (R): sequences: 5857/20932 (28.0%) reads: 11380/80353 (14.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 800/20932 (3.8%) reads: 1611/80353 (2.0%) Not mapped (no hits)(N): sequences: 4927/20932 (23.5%) reads: 39718/80353 (49.4%) Wed 30 Apr 2025 20:32:23 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1C11-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 # reads processed: 474065 # reads with at least one alignment: 276644 (58.36%) # reads that failed to align: 197421 (41.64%) Reported 816873 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 57/239 (23.8%) reads: 69/335 (20.6%) Multi-mapped placed with guidance (P): sequences: 7/239 (2.9%) reads: 8/335 (2.4%) Multi-mapped randomly placed (R): sequences: 54/239 (22.6%) reads: 60/335 (17.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 7/239 (2.9%) reads: 9/335 (2.7%) Not mapped (no hits)(N): sequences: 114/239 (47.7%) reads: 189/335 (56.4%) Wed 30 Apr 2025 20:32:24 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1C12-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: 3013462 # reads with at least one alignment: 2091937 (69.42%) # reads that failed to align: 921525 (30.58%) Reported 6384424 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 144785/474065 (30.5%) reads: 418564/1421752 (29.4%) Multi-mapped placed with guidance (P): sequences: 53075/474065 (11.2%) reads: 181941/1421752 (12.8%) Multi-mapped randomly placed (R): sequences: 70787/474065 (14.9%) reads: 200199/1421752 (14.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 7997/474065 (1.7%) reads: 140854/1421752 (9.9%) Not mapped (no hits)(N): sequences: 197421/474065 (41.6%) reads: 480194/1421752 (33.8%) Wed 30 Apr 2025 20:32:44 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1C5-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 4 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 10955 # reads with at least one alignment: 8786 (80.20%) # reads that failed to align: 2169 (19.80%) Reported 21005 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1117684/3013462 (37.1%) reads: 10190143/28121286 (36.2%) Multi-mapped placed with guidance (P): sequences: 484712/3013462 (16.1%) reads: 6031428/28121286 (21.4%) Multi-mapped randomly placed (R): sequences: 425770/3013462 (14.1%) reads: 3221807/28121286 (11.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 63771/3013462 (2.1%) reads: 2491234/28121286 (8.9%) Not mapped (no hits)(N): sequences: 921525/3013462 (30.6%) reads: 6186674/28121286 (22.0%) Wed 30 Apr 2025 20:35:17 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1C6-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: 29192 # reads with at least one alignment: 22200 (76.05%) # reads that failed to align: 6992 (23.95%) Reported 73248 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 5311/10955 (48.5%) reads: 9413/20668 (45.5%) Multi-mapped placed with guidance (P): sequences: 817/10955 (7.5%) reads: 2160/20668 (10.5%) Multi-mapped randomly placed (R): sequences: 2458/10955 (22.4%) reads: 4394/20668 (21.3%) Very highly multi-mapped (>=20 hits)(H): sequences: 200/10955 (1.8%) reads: 434/20668 (2.1%) Not mapped (no hits)(N): sequences: 2169/10955 (19.8%) reads: 4267/20668 (20.6%) Wed 30 Apr 2025 20:35:19 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1D12-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: 1305264 # reads with at least one alignment: 384500 (29.46%) # reads that failed to align: 920764 (70.54%) Reported 1009476 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 11462/29192 (39.3%) reads: 27904/118997 (23.4%) Multi-mapped placed with guidance (P): sequences: 1878/29192 (6.4%) reads: 13325/118997 (11.2%) Multi-mapped randomly placed (R): sequences: 7920/29192 (27.1%) reads: 15671/118997 (13.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 940/29192 (3.2%) reads: 1896/118997 (1.6%) Not mapped (no hits)(N): sequences: 6992/29192 (24.0%) reads: 60201/118997 (50.6%) Wed 30 Apr 2025 20:35:22 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1D1-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: 4167574 # reads with at least one alignment: 2999692 (71.98%) # reads that failed to align: 1167882 (28.02%) Reported 8787195 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 201463/1305264 (15.4%) reads: 2728816/10330343 (26.4%) Multi-mapped placed with guidance (P): sequences: 94490/1305264 (7.2%) reads: 2369766/10330343 (22.9%) Multi-mapped randomly placed (R): sequences: 79718/1305264 (6.1%) reads: 933860/10330343 (9.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 8829/1305264 (0.7%) reads: 47189/10330343 (0.5%) Not mapped (no hits)(N): sequences: 920764/1305264 (70.5%) reads: 4250712/10330343 (41.1%) Wed 30 Apr 2025 20:36:10 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1D2-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 5 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 2460790 # reads with at least one alignment: 1529828 (62.17%) # reads that failed to align: 930962 (37.83%) Reported 4519477 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1644269/4167574 (39.5%) reads: 12476963/32445753 (38.5%) Multi-mapped placed with guidance (P): sequences: 695504/4167574 (16.7%) reads: 6997606/32445753 (21.6%) Multi-mapped randomly placed (R): sequences: 576875/4167574 (13.8%) reads: 4048354/32445753 (12.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 83044/4167574 (2.0%) reads: 3263966/32445753 (10.1%) Not mapped (no hits)(N): sequences: 1167882/4167574 (28.0%) reads: 5658864/32445753 (17.4%) Wed 30 Apr 2025 20:39:32 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1D5-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: 1205093 # reads with at least one alignment: 896745 (74.41%) # reads that failed to align: 308348 (25.59%) Reported 2769666 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 834648/2460790 (33.9%) reads: 4079924/11415977 (35.7%) Multi-mapped placed with guidance (P): sequences: 339288/2460790 (13.8%) reads: 2428548/11415977 (21.3%) Multi-mapped randomly placed (R): sequences: 305634/2460790 (12.4%) reads: 1374079/11415977 (12.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 50258/2460790 (2.0%) reads: 447385/11415977 (3.9%) Not mapped (no hits)(N): sequences: 930962/2460790 (37.8%) reads: 3086041/11415977 (27.0%) Wed 30 Apr 2025 20:41:17 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1D7-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: 23774 # reads with at least one alignment: 17525 (73.71%) # reads that failed to align: 6249 (26.29%) Reported 56015 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 485342/1205093 (40.3%) reads: 2208834/7611864 (29.0%) Multi-mapped placed with guidance (P): sequences: 183321/1205093 (15.2%) reads: 1016510/7611864 (13.4%) Multi-mapped randomly placed (R): sequences: 197215/1205093 (16.4%) reads: 711847/7611864 (9.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 30867/1205093 (2.6%) reads: 318688/7611864 (4.2%) Not mapped (no hits)(N): sequences: 308348/1205093 (25.6%) reads: 3355985/7611864 (44.1%) Wed 30 Apr 2025 20:42:29 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1E7-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: 945948 # reads with at least one alignment: 697215 (73.71%) # reads that failed to align: 248733 (26.29%) Reported 2070176 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 9230/23774 (38.8%) reads: 26227/82475 (31.8%) Multi-mapped placed with guidance (P): sequences: 1599/23774 (6.7%) reads: 6573/82475 (8.0%) Multi-mapped randomly placed (R): sequences: 5977/23774 (25.1%) reads: 13778/82475 (16.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 719/23774 (3.0%) reads: 1719/82475 (2.1%) Not mapped (no hits)(N): sequences: 6249/23774 (26.3%) reads: 34178/82475 (41.4%) Wed 30 Apr 2025 20:42:32 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1F10-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: 4237921 # reads with at least one alignment: 2919256 (68.88%) # reads that failed to align: 1318665 (31.12%) Reported 8716863 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 371837/945948 (39.3%) reads: 1682093/4240284 (39.7%) Multi-mapped placed with guidance (P): sequences: 137509/945948 (14.5%) reads: 734335/4240284 (17.3%) Multi-mapped randomly placed (R): sequences: 169288/945948 (17.9%) reads: 615870/4240284 (14.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 18581/945948 (2.0%) reads: 391702/4240284 (9.2%) Not mapped (no hits)(N): sequences: 248733/945948 (26.3%) reads: 816284/4240284 (19.3%) Wed 30 Apr 2025 20:43:35 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1F12-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 5 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 66436 # reads with at least one alignment: 50755 (76.40%) # reads that failed to align: 15681 (23.60%) Reported 160359 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1597654/4237921 (37.7%) reads: 11328006/32227402 (35.2%) Multi-mapped placed with guidance (P): sequences: 679485/4237921 (16.0%) reads: 6244875/32227402 (19.4%) Multi-mapped randomly placed (R): sequences: 554298/4237921 (13.1%) reads: 3576251/32227402 (11.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 87819/4237921 (2.1%) reads: 3578713/32227402 (11.1%) Not mapped (no hits)(N): sequences: 1318665/4237921 (31.1%) reads: 7499557/32227402 (23.3%) Wed 30 Apr 2025 20:46:55 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1F1-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: 2270592 # reads with at least one alignment: 1458548 (64.24%) # reads that failed to align: 812044 (35.76%) Reported 4553794 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 26308/66436 (39.6%) reads: 65575/189542 (34.6%) Multi-mapped placed with guidance (P): sequences: 6326/66436 (9.5%) reads: 21700/189542 (11.4%) Multi-mapped randomly placed (R): sequences: 16257/66436 (24.5%) reads: 41075/189542 (21.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 1864/66436 (2.8%) reads: 11603/189542 (6.1%) Not mapped (no hits)(N): sequences: 15681/66436 (23.6%) reads: 49589/189542 (26.2%) Wed 30 Apr 2025 20:47:01 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1F3-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: 2406216 # reads with at least one alignment: 1853805 (77.04%) # reads that failed to align: 552411 (22.96%) Reported 5870353 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 779302/2270592 (34.3%) reads: 12652947/31683274 (39.9%) Multi-mapped placed with guidance (P): sequences: 327187/2270592 (14.4%) reads: 4655528/31683274 (14.7%) Multi-mapped randomly placed (R): sequences: 301252/2270592 (13.3%) reads: 2257462/31683274 (7.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 50807/2270592 (2.2%) reads: 1242984/31683274 (3.9%) Not mapped (no hits)(N): sequences: 812044/2270592 (35.8%) reads: 10874353/31683274 (34.3%) Wed 30 Apr 2025 20:48:55 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1F6-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: 277245 # reads with at least one alignment: 179815 (64.86%) # reads that failed to align: 97430 (35.14%) Reported 546593 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 967288/2406216 (40.2%) reads: 4646526/13238710 (35.1%) Multi-mapped placed with guidance (P): sequences: 434383/2406216 (18.1%) reads: 2838213/13238710 (21.4%) Multi-mapped randomly placed (R): sequences: 387930/2406216 (16.1%) reads: 1496605/13238710 (11.3%) Very highly multi-mapped (>=20 hits)(H): sequences: 64204/2406216 (2.7%) reads: 731924/13238710 (5.5%) Not mapped (no hits)(N): sequences: 552411/2406216 (23.0%) reads: 3525442/13238710 (26.6%) Wed 30 Apr 2025 20:51:17 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1F7-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: 2074259 # reads with at least one alignment: 1268873 (61.17%) # reads that failed to align: 805386 (38.83%) Reported 3566885 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 99643/277245 (35.9%) reads: 1096253/2090363 (52.4%) Multi-mapped placed with guidance (P): sequences: 27322/277245 (9.9%) reads: 162564/2090363 (7.8%) Multi-mapped randomly placed (R): sequences: 46450/277245 (16.8%) reads: 150013/2090363 (7.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 6400/277245 (2.3%) reads: 33024/2090363 (1.6%) Not mapped (no hits)(N): sequences: 97430/277245 (35.1%) reads: 648509/2090363 (31.0%) Wed 30 Apr 2025 20:51:34 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1G10-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: 4268081 # reads with at least one alignment: 3060255 (71.70%) # reads that failed to align: 1207826 (28.30%) Reported 9135162 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 730388/2074259 (35.2%) reads: 5512691/30906208 (17.8%) Multi-mapped placed with guidance (P): sequences: 254568/2074259 (12.3%) reads: 2408401/30906208 (7.8%) Multi-mapped randomly placed (R): sequences: 248497/2074259 (12.0%) reads: 1495664/30906208 (4.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 35420/2074259 (1.7%) reads: 15518154/30906208 (50.2%) Not mapped (no hits)(N): sequences: 805386/2074259 (38.8%) reads: 5971298/30906208 (19.3%) Wed 30 Apr 2025 20:53:18 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1G1-fastp-adapters-polyG-31bp-merged_condensed.fa First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 5 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 151337 # reads with at least one alignment: 96459 (63.74%) # reads that failed to align: 54878 (36.26%) Reported 287207 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1684739/4268081 (39.5%) reads: 12629106/29950754 (42.2%) Multi-mapped placed with guidance (P): sequences: 722416/4268081 (16.9%) reads: 6066042/29950754 (20.3%) Multi-mapped randomly placed (R): sequences: 563447/4268081 (13.2%) reads: 3489891/29950754 (11.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 89653/4268081 (2.1%) reads: 1679694/29950754 (5.6%) Not mapped (no hits)(N): sequences: 1207826/4268081 (28.3%) reads: 6086021/29950754 (20.3%) Wed 30 Apr 2025 20:56:41 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1G3-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: 284604 # reads with at least one alignment: 191475 (67.28%) # reads that failed to align: 93129 (32.72%) Reported 562942 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 52993/151337 (35.0%) reads: 255316/840423 (30.4%) Multi-mapped placed with guidance (P): sequences: 13487/151337 (8.9%) reads: 84242/840423 (10.0%) Multi-mapped randomly placed (R): sequences: 26657/151337 (17.6%) reads: 116850/840423 (13.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 3322/151337 (2.2%) reads: 21274/840423 (2.5%) Not mapped (no hits)(N): sequences: 54878/151337 (36.3%) reads: 362741/840423 (43.2%) Wed 30 Apr 2025 20:56:50 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1H1-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: 94503 # reads with at least one alignment: 61655 (65.24%) # reads that failed to align: 32848 (34.76%) Reported 178752 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 103191/284604 (36.3%) reads: 598703/1579950 (37.9%) Multi-mapped placed with guidance (P): sequences: 32316/284604 (11.4%) reads: 257565/1579950 (16.3%) Multi-mapped randomly placed (R): sequences: 49708/284604 (17.5%) reads: 183324/1579950 (11.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 6260/284604 (2.2%) reads: 34460/1579950 (2.2%) Not mapped (no hits)(N): sequences: 93129/284604 (32.7%) reads: 505898/1579950 (32.0%) Wed 30 Apr 2025 20:57:00 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1H2-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: 107691 # reads with at least one alignment: 74623 (69.29%) # reads that failed to align: 33068 (30.71%) Reported 178273 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 33890/94503 (35.9%) reads: 188240/541044 (34.8%) Multi-mapped placed with guidance (P): sequences: 7992/94503 (8.5%) reads: 54440/541044 (10.1%) Multi-mapped randomly placed (R): sequences: 17844/94503 (18.9%) reads: 70536/541044 (13.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 1929/94503 (2.0%) reads: 10790/541044 (2.0%) Not mapped (no hits)(N): sequences: 32848/94503 (34.8%) reads: 217038/541044 (40.1%) Wed 30 Apr 2025 20:57:03 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/1H3-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: 36678 # reads with at least one alignment: 9876 (26.93%) # reads that failed to align: 26802 (73.07%) Reported 42452 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 46952/107691 (43.6%) reads: 496262/896907 (55.3%) Multi-mapped placed with guidance (P): sequences: 9722/107691 (9.0%) reads: 97856/896907 (10.9%) Multi-mapped randomly placed (R): sequences: 16364/107691 (15.2%) reads: 75024/896907 (8.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 1585/107691 (1.5%) reads: 18135/896907 (2.0%) Not mapped (no hits)(N): sequences: 33068/107691 (30.7%) reads: 209630/896907 (23.4%) Wed 30 Apr 2025 20:57:07 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2A3-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: 2544108 # reads with at least one alignment: 1630926 (64.11%) # reads that failed to align: 913182 (35.89%) Reported 4851249 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 3737/36678 (10.2%) reads: 12511/84474 (14.8%) Multi-mapped placed with guidance (P): sequences: 2595/36678 (7.1%) reads: 4440/84474 (5.3%) Multi-mapped randomly placed (R): sequences: 2882/36678 (7.9%) reads: 4080/84474 (4.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 662/36678 (1.8%) reads: 1019/84474 (1.2%) Not mapped (no hits)(N): sequences: 26802/36678 (73.1%) reads: 62424/84474 (73.9%) Wed 30 Apr 2025 20:57:09 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2B1-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: 1029513 # reads with at least one alignment: 699926 (67.99%) # reads that failed to align: 329587 (32.01%) Reported 2184986 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 886972/2544108 (34.9%) reads: 3916522/13670578 (28.6%) Multi-mapped placed with guidance (P): sequences: 365394/2544108 (14.4%) reads: 2127667/13670578 (15.6%) Multi-mapped randomly placed (R): sequences: 328081/2544108 (12.9%) reads: 1375712/13670578 (10.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 50479/2544108 (2.0%) reads: 819467/13670578 (6.0%) Not mapped (no hits)(N): sequences: 913182/2544108 (35.9%) reads: 5431210/13670578 (39.7%) Wed 30 Apr 2025 20:58:13 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2D1-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: 34364 # reads with at least one alignment: 9284 (27.02%) # reads that failed to align: 25080 (72.98%) Reported 37800 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 385118/1029513 (37.4%) reads: 3126243/11470292 (27.3%) Multi-mapped placed with guidance (P): sequences: 128706/1029513 (12.5%) reads: 1015112/11470292 (8.8%) Multi-mapped randomly placed (R): sequences: 159348/1029513 (15.5%) reads: 802814/11470292 (7.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 26754/1029513 (2.6%) reads: 220565/11470292 (1.9%) Not mapped (no hits)(N): sequences: 329587/1029513 (32.0%) reads: 6305558/11470292 (55.0%) Wed 30 Apr 2025 20:59:14 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2D3-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: 599863 # reads with at least one alignment: 394827 (65.82%) # reads that failed to align: 205036 (34.18%) Reported 1165244 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 3579/34364 (10.4%) reads: 8097/58131 (13.9%) Multi-mapped placed with guidance (P): sequences: 2476/34364 (7.2%) reads: 4107/58131 (7.1%) Multi-mapped randomly placed (R): sequences: 2694/34364 (7.8%) reads: 3652/58131 (6.3%) Very highly multi-mapped (>=20 hits)(H): sequences: 535/34364 (1.6%) reads: 770/58131 (1.3%) Not mapped (no hits)(N): sequences: 25080/34364 (73.0%) reads: 41505/58131 (71.4%) Wed 30 Apr 2025 20:59:16 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2E1-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: 83 # reads with at least one alignment: 19 (22.89%) # reads that failed to align: 64 (77.11%) Reported 141 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 227184/599863 (37.9%) reads: 2858880/11237440 (25.4%) Multi-mapped placed with guidance (P): sequences: 60146/599863 (10.0%) reads: 1020127/11237440 (9.1%) Multi-mapped randomly placed (R): sequences: 93045/599863 (15.5%) reads: 989891/11237440 (8.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 14452/599863 (2.4%) reads: 177829/11237440 (1.6%) Not mapped (no hits)(N): sequences: 205036/599863 (34.2%) reads: 6190713/11237440 (55.1%) Wed 30 Apr 2025 20:59:52 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2E3-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 # reads processed: 28062 # reads with at least one alignment: 18073 (64.40%) # reads that failed to align: 9989 (35.60%) Reported 42814 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 7/83 (8.4%) reads: 7/95 (7.4%) Multi-mapped placed with guidance (P): sequences: 0/83 (0.0%) reads: 0/95 (0.0%) Multi-mapped randomly placed (R): sequences: 7/83 (8.4%) reads: 8/95 (8.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 5/83 (6.0%) reads: 10/95 (10.5%) Not mapped (no hits)(N): sequences: 64/83 (77.1%) reads: 70/95 (73.7%) Wed 30 Apr 2025 20:59:55 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2F2-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: 2956 # reads with at least one alignment: 613 (20.74%) # reads that failed to align: 2343 (79.26%) Reported 2834 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 11272/28062 (40.2%) reads: 21781/63669 (34.2%) Multi-mapped placed with guidance (P): sequences: 1782/28062 (6.4%) reads: 5986/63669 (9.4%) Multi-mapped randomly placed (R): sequences: 4584/28062 (16.3%) reads: 10441/63669 (16.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 435/28062 (1.6%) reads: 926/63669 (1.5%) Not mapped (no hits)(N): sequences: 9989/28062 (35.6%) reads: 24535/63669 (38.5%) Wed 30 Apr 2025 21:00:06 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2H1-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: 1799671 # reads with at least one alignment: 1299176 (72.19%) # reads that failed to align: 500495 (27.81%) Reported 4083415 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 273/2956 (9.2%) reads: 388/5450 (7.1%) Multi-mapped placed with guidance (P): sequences: 65/2956 (2.2%) reads: 79/5450 (1.4%) Multi-mapped randomly placed (R): sequences: 216/2956 (7.3%) reads: 283/5450 (5.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 59/2956 (2.0%) reads: 331/5450 (6.1%) Not mapped (no hits)(N): sequences: 2343/2956 (79.3%) reads: 4369/5450 (80.2%) Wed 30 Apr 2025 21:00:11 -0700 PDT Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/2H2-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: 694455/1799671 (38.6%) reads: 4078249/13183489 (30.9%) Multi-mapped placed with guidance (P): sequences: 273716/1799671 (15.2%) reads: 1759809/13183489 (13.3%) Multi-mapped randomly placed (R): sequences: 283682/1799671 (15.8%) reads: 1264817/13183489 (9.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 47323/1799671 (2.6%) reads: 829135/13183489 (6.3%) Not mapped (no hits)(N): sequences: 500495/1799671 (27.8%) reads: 5251479/13183489 (39.8%) Wed 30 Apr 2025 21:01:35 -0700 PDT Merging and indexing alignments Wed 30 Apr 2025 21:04:58 -0700 PDT Defining small RNA clusters de novo With 313815901 total reads and mincov of 1 reads per million, the min read depth is 314 Wed 30 Apr 2025 21:05:43 -0700 PDT Analyzing cluster properties using 40 threads # reads processed: 49415 # reads with at least one alignment: 133 (0.27%) # reads that failed to align: 49282 (99.73%) Reported 2562 alignments [bam_sort_core] merging from 0 files and 40 in-memory blocks... Wed 30 Apr 2025 21:06:59 -0700 PDT Completed Wed 30 Apr 2025 21:06:59 -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 21:07:31 -0700 PDT Analyzing cluster properties using 40 threads Wed 30 Apr 2025 21:07:31 -0700 PDT Completed Writing final files Found a total of 48 MIRNA loci Non-MIRNA loci by DicerCall: N 15578 23 25 22 18 24 18 21 16 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 21:07:51 -0700 PDT Run Completed! real 88m46.039s user 718m8.580s sys 217m50.551s