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/D-Apul/data/Apulchra-genome.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/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A10-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A12-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A8-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1A9-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B10-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B5-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1B9-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C10-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1C4-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D10-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D4-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D6-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D8-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1D9-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E5-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1E9-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F11-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F4-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1F8-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1G5-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H11-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H12-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H6-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H7-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/1H8-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2B2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2B3-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2C1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2C2-fastp-adapters-polyG-31bp-merged.fq.gz', # reads processed: 1089229 # reads with at least one alignment: 738135 (67.77%) # reads that failed to align: 351094 (32.23%) Reported 4242347 alignments '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2D2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2E2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2F1-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/01.10-D-Apul-sRNAseq-trimming-fastp-FastQC-MultiQC/trimmed-fastqs-sRNA/2G1-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 Fri 20 Dec 2024 18:32:49 -0800 PST Condensing reads Beginning alignment phase Fri 20 Dec 2024 18:56:37 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1A10-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: 1272465 # reads with at least one alignment: 970474 (76.27%) # reads that failed to align: 301991 (23.73%) Reported 4704557 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 323431/1089229 (29.7%) reads: 1074476/5951493 (18.1%) Multi-mapped placed with guidance (P): sequences: 163922/1089229 (15.0%) reads: 846730/5951493 (14.2%) Multi-mapped randomly placed (R): sequences: 135213/1089229 (12.4%) reads: 337421/5951493 (5.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 115569/1089229 (10.6%) reads: 1882383/5951493 (31.6%) Not mapped (no hits)(N): sequences: 351094/1089229 (32.2%) reads: 1810483/5951493 (30.4%) Fri 20 Dec 2024 18:57:27 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1A12-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: 1558385 # reads with at least one alignment: 1050856 (67.43%) # reads that failed to align: 507529 (32.57%) Reported 5396384 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 437246/1272465 (34.4%) reads: 2127437/6183357 (34.4%) Multi-mapped placed with guidance (P): sequences: 261828/1272465 (20.6%) reads: 1451191/6183357 (23.5%) Multi-mapped randomly placed (R): sequences: 168671/1272465 (13.3%) reads: 507434/6183357 (8.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 102729/1272465 (8.1%) reads: 664171/6183357 (10.7%) Not mapped (no hits)(N): sequences: 301991/1272465 (23.7%) reads: 1433124/6183357 (23.2%) Fri 20 Dec 2024 18:58:16 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1A1-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: 2017013 # reads with at least one alignment: 1445065 (71.64%) # reads that failed to align: 571948 (28.36%) Reported 6953927 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 461570/1558385 (29.6%) reads: 2510372/8707352 (28.8%) Multi-mapped placed with guidance (P): sequences: 290494/1558385 (18.6%) reads: 1939561/8707352 (22.3%) Multi-mapped randomly placed (R): sequences: 173885/1558385 (11.2%) reads: 552343/8707352 (6.3%) Very highly multi-mapped (>=20 hits)(H): sequences: 124907/1558385 (8.0%) reads: 1218750/8707352 (14.0%) Not mapped (no hits)(N): sequences: 507529/1558385 (32.6%) reads: 2486326/8707352 (28.6%) Fri 20 Dec 2024 18:59:07 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1A2-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: 1485596 # reads with at least one alignment: 1092763 (73.56%) # reads that failed to align: 392833 (26.44%) Reported 5265066 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 668003/2017013 (33.1%) reads: 2759128/10520192 (26.2%) Multi-mapped placed with guidance (P): sequences: 393235/2017013 (19.5%) reads: 2021359/10520192 (19.2%) Multi-mapped randomly placed (R): sequences: 232765/2017013 (11.5%) reads: 633400/10520192 (6.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 151062/2017013 (7.5%) reads: 1683046/10520192 (16.0%) Not mapped (no hits)(N): sequences: 571948/2017013 (28.4%) reads: 3423259/10520192 (32.5%) Fri 20 Dec 2024 19:00:07 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1A8-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: 2533167 # reads with at least one alignment: 1756521 (69.34%) # reads that failed to align: 776646 (30.66%) Reported 8058195 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 539842/1485596 (36.3%) reads: 2200417/7769703 (28.3%) Multi-mapped placed with guidance (P): sequences: 252268/1485596 (17.0%) reads: 1379644/7769703 (17.8%) Multi-mapped randomly placed (R): sequences: 176841/1485596 (11.9%) reads: 491174/7769703 (6.3%) Very highly multi-mapped (>=20 hits)(H): sequences: 123812/1485596 (8.3%) reads: 1835559/7769703 (23.6%) Not mapped (no hits)(N): sequences: 392833/1485596 (26.4%) reads: 1862909/7769703 (24.0%) Fri 20 Dec 2024 19:00:59 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1A9-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: 1350448 # reads with at least one alignment: 845311 (62.59%) # reads that failed to align: 505137 (37.41%) Reported 4574454 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 809571/2533167 (32.0%) reads: 3951224/13617875 (29.0%) Multi-mapped placed with guidance (P): sequences: 510841/2533167 (20.2%) reads: 2859375/13617875 (21.0%) Multi-mapped randomly placed (R): sequences: 279589/2533167 (11.0%) reads: 904765/13617875 (6.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 156520/2533167 (6.2%) reads: 1083154/13617875 (8.0%) Not mapped (no hits)(N): sequences: 776646/2533167 (30.7%) reads: 4819357/13617875 (35.4%) Fri 20 Dec 2024 19:02:11 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1B10-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: 1677356 # reads with at least one alignment: 985303 (58.74%) # reads that failed to align: 692053 (41.26%) Reported 5216274 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 393313/1350448 (29.1%) reads: 1637574/6911300 (23.7%) Multi-mapped placed with guidance (P): sequences: 184186/1350448 (13.6%) reads: 1028238/6911300 (14.9%) Multi-mapped randomly placed (R): sequences: 143273/1350448 (10.6%) reads: 340635/6911300 (4.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 124539/1350448 (9.2%) reads: 1675375/6911300 (24.2%) Not mapped (no hits)(N): sequences: 505137/1350448 (37.4%) reads: 2229478/6911300 (32.3%) Fri 20 Dec 2024 19:03:02 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1B1-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: 1552923 # reads with at least one alignment: 873733 (56.26%) # reads that failed to align: 679190 (43.74%) Reported 4674478 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 461764/1677356 (27.5%) reads: 2036402/9060831 (22.5%) Multi-mapped placed with guidance (P): sequences: 218546/1677356 (13.0%) reads: 1304472/9060831 (14.4%) Multi-mapped randomly placed (R): sequences: 170765/1677356 (10.2%) reads: 450012/9060831 (5.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 134228/1677356 (8.0%) reads: 1858550/9060831 (20.5%) Not mapped (no hits)(N): sequences: 692053/1677356 (41.3%) reads: 3411395/9060831 (37.6%) Fri 20 Dec 2024 19:03:53 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1B2-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: 2803701 # reads with at least one alignment: 2132502 (76.06%) # reads that failed to align: 671199 (23.94%) Reported 10091437 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 396187/1552923 (25.5%) reads: 1892077/9380119 (20.2%) Multi-mapped placed with guidance (P): sequences: 207112/1552923 (13.3%) reads: 1516594/9380119 (16.2%) Multi-mapped randomly placed (R): sequences: 150067/1552923 (9.7%) reads: 441586/9380119 (4.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 120367/1552923 (7.8%) reads: 1994837/9380119 (21.3%) Not mapped (no hits)(N): sequences: 679190/1552923 (43.7%) reads: 3535025/9380119 (37.7%) Fri 20 Dec 2024 19:04:39 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1B5-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: 1239555 # reads with at least one alignment: 802489 (64.74%) # reads that failed to align: 437066 (35.26%) Reported 4765213 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 974736/2803701 (34.8%) reads: 4644851/12874226 (36.1%) Multi-mapped placed with guidance (P): sequences: 666862/2803701 (23.8%) reads: 3631041/12874226 (28.2%) Multi-mapped randomly placed (R): sequences: 285356/2803701 (10.2%) reads: 968483/12874226 (7.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 205548/2803701 (7.3%) reads: 1504877/12874226 (11.7%) Not mapped (no hits)(N): sequences: 671199/2803701 (23.9%) reads: 2124974/12874226 (16.5%) Fri 20 Dec 2024 19:06:02 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1B9-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: 1379817 # reads with at least one alignment: 623676 (45.20%) # reads that failed to align: 756141 (54.80%) Reported 3905159 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 338513/1239555 (27.3%) reads: 1120120/6836685 (16.4%) Multi-mapped placed with guidance (P): sequences: 186699/1239555 (15.1%) reads: 918578/6836685 (13.4%) Multi-mapped randomly placed (R): sequences: 145983/1239555 (11.8%) reads: 329904/6836685 (4.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 131294/1239555 (10.6%) reads: 2267874/6836685 (33.2%) Not mapped (no hits)(N): sequences: 437066/1239555 (35.3%) reads: 2200209/6836685 (32.2%) Fri 20 Dec 2024 19:06:54 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1C10-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: 1821985 # reads with at least one alignment: 800189 (43.92%) # reads that failed to align: 1021796 (56.08%) Reported 5480637 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 275893/1379817 (20.0%) reads: 979838/6142279 (16.0%) Multi-mapped placed with guidance (P): sequences: 118218/1379817 (8.6%) reads: 753083/6142279 (12.3%) Multi-mapped randomly placed (R): sequences: 108808/1379817 (7.9%) reads: 246337/6142279 (4.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 120757/1379817 (8.8%) reads: 1321973/6142279 (21.5%) Not mapped (no hits)(N): sequences: 756141/1379817 (54.8%) reads: 2841048/6142279 (46.3%) Fri 20 Dec 2024 19:07:38 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1C4-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: 1896137 # reads with at least one alignment: 1445774 (76.25%) # reads that failed to align: 450363 (23.75%) Reported 7335520 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 349801/1821985 (19.2%) reads: 1123527/10192438 (11.0%) Multi-mapped placed with guidance (P): sequences: 133176/1821985 (7.3%) reads: 642635/10192438 (6.3%) Multi-mapped randomly placed (R): sequences: 135423/1821985 (7.4%) reads: 352498/10192438 (3.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 181789/1821985 (10.0%) reads: 1691403/10192438 (16.6%) Not mapped (no hits)(N): sequences: 1021796/1821985 (56.1%) reads: 6382375/10192438 (62.6%) Fri 20 Dec 2024 19:08:33 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1D10-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: 2543995 # reads with at least one alignment: 1888911 (74.25%) # reads that failed to align: 655084 (25.75%) Reported 9585840 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 635258/1896137 (33.5%) reads: 2550937/8008657 (31.9%) Multi-mapped placed with guidance (P): sequences: 419740/1896137 (22.1%) reads: 2075216/8008657 (25.9%) Multi-mapped randomly placed (R): sequences: 226642/1896137 (12.0%) reads: 639146/8008657 (8.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 164134/1896137 (8.7%) reads: 1167223/8008657 (14.6%) Not mapped (no hits)(N): sequences: 450363/1896137 (23.8%) reads: 1576135/8008657 (19.7%) Fri 20 Dec 2024 19:09:40 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1D3-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: 2190860 # reads with at least one alignment: 1590409 (72.59%) # reads that failed to align: 600451 (27.41%) Reported 7624802 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 805973/2543995 (31.7%) reads: 4878669/15206541 (32.1%) Multi-mapped placed with guidance (P): sequences: 601277/2543995 (23.6%) reads: 3965033/15206541 (26.1%) Multi-mapped randomly placed (R): sequences: 275786/2543995 (10.8%) reads: 1041448/15206541 (6.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 205875/2543995 (8.1%) reads: 2100025/15206541 (13.8%) Not mapped (no hits)(N): sequences: 655084/2543995 (25.8%) reads: 3221366/15206541 (21.2%) Fri 20 Dec 2024 19:11:01 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1D4-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: 2314604 # reads with at least one alignment: 1839986 (79.49%) # reads that failed to align: 474618 (20.51%) Reported 8372116 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 735121/2190860 (33.6%) reads: 3421296/11513063 (29.7%) Multi-mapped placed with guidance (P): sequences: 444780/2190860 (20.3%) reads: 2410146/11513063 (20.9%) Multi-mapped randomly placed (R): sequences: 241889/2190860 (11.0%) reads: 759873/11513063 (6.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 168619/2190860 (7.7%) reads: 1712399/11513063 (14.9%) Not mapped (no hits)(N): sequences: 600451/2190860 (27.4%) reads: 3209349/11513063 (27.9%) Fri 20 Dec 2024 19:12:14 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1D6-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: 1406289 # reads with at least one alignment: 1060008 (75.38%) # reads that failed to align: 346281 (24.62%) Reported 4960753 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 869752/2314604 (37.6%) reads: 4989943/13917067 (35.9%) Multi-mapped placed with guidance (P): sequences: 535806/2314604 (23.1%) reads: 3568134/13917067 (25.6%) Multi-mapped randomly placed (R): sequences: 269873/2314604 (11.7%) reads: 1183812/13917067 (8.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 164555/2314604 (7.1%) reads: 1568126/13917067 (11.3%) Not mapped (no hits)(N): sequences: 474618/2314604 (20.5%) reads: 2607052/13917067 (18.7%) Fri 20 Dec 2024 19:13:25 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1D8-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: 2096079 # reads with at least one alignment: 1493088 (71.23%) # reads that failed to align: 602991 (28.77%) Reported 7323654 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 486585/1406289 (34.6%) reads: 2341390/7489968 (31.3%) Multi-mapped placed with guidance (P): sequences: 292041/1406289 (20.8%) reads: 1837532/7489968 (24.5%) Multi-mapped randomly placed (R): sequences: 177687/1406289 (12.6%) reads: 537470/7489968 (7.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 103695/1406289 (7.4%) reads: 627466/7489968 (8.4%) Not mapped (no hits)(N): sequences: 346281/1406289 (24.6%) reads: 2146110/7489968 (28.7%) Fri 20 Dec 2024 19:14:17 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1D9-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: 1834316 # reads with at least one alignment: 899472 (49.04%) # reads that failed to align: 934844 (50.96%) Reported 4767593 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 682136/2096079 (32.5%) reads: 2672336/8967034 (29.8%) Multi-mapped placed with guidance (P): sequences: 426964/2096079 (20.4%) reads: 2027958/8967034 (22.6%) Multi-mapped randomly placed (R): sequences: 220691/2096079 (10.5%) reads: 611857/8967034 (6.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 163297/2096079 (7.8%) reads: 1503535/8967034 (16.8%) Not mapped (no hits)(N): sequences: 602991/2096079 (28.8%) reads: 2151348/8967034 (24.0%) Fri 20 Dec 2024 19:15:21 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1E1-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: 2673506 # reads with at least one alignment: 2026854 (75.81%) # reads that failed to align: 646652 (24.19%) Reported 9550618 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 419375/1834316 (22.9%) reads: 1623544/10473201 (15.5%) Multi-mapped placed with guidance (P): sequences: 197765/1834316 (10.8%) reads: 1179816/10473201 (11.3%) Multi-mapped randomly placed (R): sequences: 158658/1834316 (8.6%) reads: 443538/10473201 (4.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 123674/1834316 (6.7%) reads: 1834344/10473201 (17.5%) Not mapped (no hits)(N): sequences: 934844/1834316 (51.0%) reads: 5391959/10473201 (51.5%) Fri 20 Dec 2024 19:16:09 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1E3-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: 1280675 # reads with at least one alignment: 373006 (29.13%) # reads that failed to align: 907669 (70.87%) Reported 2421496 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 959295/2673506 (35.9%) reads: 4865239/17188301 (28.3%) Multi-mapped placed with guidance (P): sequences: 581360/2673506 (21.7%) reads: 3880093/17188301 (22.6%) Multi-mapped randomly placed (R): sequences: 284323/2673506 (10.6%) reads: 1014603/17188301 (5.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 201876/2673506 (7.6%) reads: 2867588/17188301 (16.7%) Not mapped (no hits)(N): sequences: 646652/2673506 (24.2%) reads: 4560778/17188301 (26.5%) Fri 20 Dec 2024 19:17:34 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1E5-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: 1998234 # reads with at least one alignment: 1002690 (50.18%) # reads that failed to align: 995544 (49.82%) Reported 5226629 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 177346/1280675 (13.8%) reads: 479606/8005908 (6.0%) Multi-mapped placed with guidance (P): sequences: 43913/1280675 (3.4%) reads: 202828/8005908 (2.5%) Multi-mapped randomly placed (R): sequences: 71199/1280675 (5.6%) reads: 189706/8005908 (2.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 80548/1280675 (6.3%) reads: 1223950/8005908 (15.3%) Not mapped (no hits)(N): sequences: 907669/1280675 (70.9%) reads: 5909818/8005908 (73.8%) Fri 20 Dec 2024 19:18:07 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1E9-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: 1258345 # reads with at least one alignment: 840294 (66.78%) # reads that failed to align: 418051 (33.22%) Reported 4459980 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 453832/1998234 (22.7%) reads: 1730522/7877541 (22.0%) Multi-mapped placed with guidance (P): sequences: 250330/1998234 (12.5%) reads: 1203227/7877541 (15.3%) Multi-mapped randomly placed (R): sequences: 166472/1998234 (8.3%) reads: 397140/7877541 (5.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 132056/1998234 (6.6%) reads: 1298349/7877541 (16.5%) Not mapped (no hits)(N): sequences: 995544/1998234 (49.8%) reads: 3248303/7877541 (41.2%) Fri 20 Dec 2024 19:19:02 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1F11-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: 1938577 # reads with at least one alignment: 1387431 (71.57%) # reads that failed to align: 551146 (28.43%) Reported 6520814 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 397428/1258345 (31.6%) reads: 1934972/7439594 (26.0%) Multi-mapped placed with guidance (P): sequences: 176695/1258345 (14.0%) reads: 1249654/7439594 (16.8%) Multi-mapped randomly placed (R): sequences: 149825/1258345 (11.9%) reads: 491815/7439594 (6.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 116346/1258345 (9.2%) reads: 1089134/7439594 (14.6%) Not mapped (no hits)(N): sequences: 418051/1258345 (33.2%) reads: 2674019/7439594 (35.9%) Fri 20 Dec 2024 19:19:47 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1F4-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: 1091157 # reads with at least one alignment: 659877 (60.47%) # reads that failed to align: 431280 (39.53%) Reported 3593159 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 661464/1938577 (34.1%) reads: 3505495/10897549 (32.2%) Multi-mapped placed with guidance (P): sequences: 370030/1938577 (19.1%) reads: 2363676/10897549 (21.7%) Multi-mapped randomly placed (R): sequences: 211240/1938577 (10.9%) reads: 701680/10897549 (6.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 144697/1938577 (7.5%) reads: 1481979/10897549 (13.6%) Not mapped (no hits)(N): sequences: 551146/1938577 (28.4%) reads: 2844719/10897549 (26.1%) Fri 20 Dec 2024 19:20:47 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1F8-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: 2457948 # reads with at least one alignment: 1813193 (73.77%) # reads that failed to align: 644755 (26.23%) Reported 8430522 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 313519/1091157 (28.7%) reads: 976955/7066755 (13.8%) Multi-mapped placed with guidance (P): sequences: 125451/1091157 (11.5%) reads: 781439/7066755 (11.1%) Multi-mapped randomly placed (R): sequences: 123618/1091157 (11.3%) reads: 311019/7066755 (4.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 97289/1091157 (8.9%) reads: 2726762/7066755 (38.6%) Not mapped (no hits)(N): sequences: 431280/1091157 (39.5%) reads: 2270580/7066755 (32.1%) Fri 20 Dec 2024 19:21:31 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1G5-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: 1311847 # reads with at least one alignment: 868185 (66.18%) # reads that failed to align: 443662 (33.82%) Reported 4724684 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 828940/2457948 (33.7%) reads: 4099811/13186219 (31.1%) Multi-mapped placed with guidance (P): sequences: 540479/2457948 (22.0%) reads: 3018984/13186219 (22.9%) Multi-mapped randomly placed (R): sequences: 276319/2457948 (11.2%) reads: 935293/13186219 (7.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 167455/2457948 (6.8%) reads: 1445734/13186219 (11.0%) Not mapped (no hits)(N): sequences: 644755/2457948 (26.2%) reads: 3686397/13186219 (28.0%) Fri 20 Dec 2024 19:22:46 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1H11-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: 1283820 # reads with at least one alignment: 678247 (52.83%) # reads that failed to align: 605573 (47.17%) Reported 3440275 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 375429/1311847 (28.6%) reads: 1627891/5914956 (27.5%) Multi-mapped placed with guidance (P): sequences: 219756/1311847 (16.8%) reads: 1145472/5914956 (19.4%) Multi-mapped randomly placed (R): sequences: 155325/1311847 (11.8%) reads: 417778/5914956 (7.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 117675/1311847 (9.0%) reads: 1179544/5914956 (19.9%) Not mapped (no hits)(N): sequences: 443662/1311847 (33.8%) reads: 1544271/5914956 (26.1%) Fri 20 Dec 2024 19:23:41 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1H12-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: 2079178 # reads with at least one alignment: 1444872 (69.49%) # reads that failed to align: 634306 (30.51%) Reported 7074673 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 324073/1283820 (25.2%) reads: 1103200/6805833 (16.2%) Multi-mapped placed with guidance (P): sequences: 143543/1283820 (11.2%) reads: 710663/6805833 (10.4%) Multi-mapped randomly placed (R): sequences: 125273/1283820 (9.8%) reads: 297444/6805833 (4.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 85358/1283820 (6.6%) reads: 2124864/6805833 (31.2%) Not mapped (no hits)(N): sequences: 605573/1283820 (47.2%) reads: 2569662/6805833 (37.8%) Fri 20 Dec 2024 19:24:19 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1H6-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: 2116961 # reads with at least one alignment: 1680213 (79.37%) # reads that failed to align: 436748 (20.63%) Reported 8069053 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 665115/2079178 (32.0%) reads: 4291181/13603228 (31.5%) Multi-mapped placed with guidance (P): sequences: 387747/2079178 (18.6%) reads: 2916496/13603228 (21.4%) Multi-mapped randomly placed (R): sequences: 235056/2079178 (11.3%) reads: 1026145/13603228 (7.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 156954/2079178 (7.5%) reads: 1791814/13603228 (13.2%) Not mapped (no hits)(N): sequences: 634306/2079178 (30.5%) reads: 3577592/13603228 (26.3%) Fri 20 Dec 2024 19:25:27 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1H7-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: 1432666 # reads with at least one alignment: 990207 (69.12%) # reads that failed to align: 442459 (30.88%) Reported 4957465 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 759135/2116961 (35.9%) reads: 2621848/7833059 (33.5%) Multi-mapped placed with guidance (P): sequences: 484111/2116961 (22.9%) reads: 1848675/7833059 (23.6%) Multi-mapped randomly placed (R): sequences: 272913/2116961 (12.9%) reads: 680876/7833059 (8.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 164054/2116961 (7.7%) reads: 1185386/7833059 (15.1%) Not mapped (no hits)(N): sequences: 436748/2116961 (20.6%) reads: 1496274/7833059 (19.1%) Fri 20 Dec 2024 19:26:38 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/1H8-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: 2085417 # reads with at least one alignment: 1297694 (62.23%) # reads that failed to align: 787723 (37.77%) Reported 8024219 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 454242/1432666 (31.7%) reads: 1868362/7090666 (26.3%) Multi-mapped placed with guidance (P): sequences: 252353/1432666 (17.6%) reads: 1332772/7090666 (18.8%) Multi-mapped randomly placed (R): sequences: 168218/1432666 (11.7%) reads: 470743/7090666 (6.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 115394/1432666 (8.1%) reads: 1743604/7090666 (24.6%) Not mapped (no hits)(N): sequences: 442459/1432666 (30.9%) reads: 1675185/7090666 (23.6%) Fri 20 Dec 2024 19:27:26 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/2B2-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: 2327966 # reads with at least one alignment: 1710393 (73.47%) # reads that failed to align: 617573 (26.53%) Reported 8535209 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 566390/2085417 (27.2%) reads: 2089239/11611845 (18.0%) Multi-mapped placed with guidance (P): sequences: 290193/2085417 (13.9%) reads: 1639627/11611845 (14.1%) Multi-mapped randomly placed (R): sequences: 201058/2085417 (9.6%) reads: 601649/11611845 (5.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 240053/2085417 (11.5%) reads: 4058253/11611845 (34.9%) Not mapped (no hits)(N): sequences: 787723/2085417 (37.8%) reads: 3223077/11611845 (27.8%) Fri 20 Dec 2024 19:28:38 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/2B3-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: 2370018 # reads with at least one alignment: 1489166 (62.83%) # reads that failed to align: 880852 (37.17%) Reported 7357575 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 813313/2327966 (34.9%) reads: 4793698/17445188 (27.5%) Multi-mapped placed with guidance (P): sequences: 441068/2327966 (18.9%) reads: 3356903/17445188 (19.2%) Multi-mapped randomly placed (R): sequences: 255475/2327966 (11.0%) reads: 993025/17445188 (5.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 200537/2327966 (8.6%) reads: 3808825/17445188 (21.8%) Not mapped (no hits)(N): sequences: 617573/2327966 (26.5%) reads: 4492737/17445188 (25.8%) Fri 20 Dec 2024 19:29:54 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/2C1-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: 2418191 # reads with at least one alignment: 1894936 (78.36%) # reads that failed to align: 523255 (21.64%) Reported 9278129 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 695977/2370018 (29.4%) reads: 3131917/13442566 (23.3%) Multi-mapped placed with guidance (P): sequences: 391782/2370018 (16.5%) reads: 2318399/13442566 (17.2%) Multi-mapped randomly placed (R): sequences: 230400/2370018 (9.7%) reads: 634706/13442566 (4.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 171007/2370018 (7.2%) reads: 3161704/13442566 (23.5%) Not mapped (no hits)(N): sequences: 880852/2370018 (37.2%) reads: 4195840/13442566 (31.2%) Fri 20 Dec 2024 19:31:03 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/2C2-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: 1971103 # reads with at least one alignment: 1059121 (53.73%) # reads that failed to align: 911982 (46.27%) Reported 5856824 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 846809/2418191 (35.0%) reads: 4793574/15759131 (30.4%) Multi-mapped placed with guidance (P): sequences: 561992/2418191 (23.2%) reads: 3722029/15759131 (23.6%) Multi-mapped randomly placed (R): sequences: 290441/2418191 (12.0%) reads: 1023453/15759131 (6.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 195694/2418191 (8.1%) reads: 2123717/15759131 (13.5%) Not mapped (no hits)(N): sequences: 523255/2418191 (21.6%) reads: 4096358/15759131 (26.0%) Fri 20 Dec 2024 19:32:21 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/2D2-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: 1610113 # reads with at least one alignment: 852988 (52.98%) # reads that failed to align: 757125 (47.02%) Reported 5698211 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 485769/1971103 (24.6%) reads: 2001371/11056415 (18.1%) Multi-mapped placed with guidance (P): sequences: 240851/1971103 (12.2%) reads: 1377470/11056415 (12.5%) Multi-mapped randomly placed (R): sequences: 170684/1971103 (8.7%) reads: 405611/11056415 (3.7%) Very highly multi-mapped (>=20 hits)(H): sequences: 161817/1971103 (8.2%) reads: 2165525/11056415 (19.6%) Not mapped (no hits)(N): sequences: 911982/1971103 (46.3%) reads: 5106438/11056415 (46.2%) Fri 20 Dec 2024 19:33:19 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/2E2-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: 1838887 # reads with at least one alignment: 1146323 (62.34%) # reads that failed to align: 692564 (37.66%) Reported 8085259 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 398797/1610113 (24.8%) reads: 1259932/11769125 (10.7%) Multi-mapped placed with guidance (P): sequences: 131907/1610113 (8.2%) reads: 1355026/11769125 (11.5%) Multi-mapped randomly placed (R): sequences: 129107/1610113 (8.0%) reads: 290388/11769125 (2.5%) Very highly multi-mapped (>=20 hits)(H): sequences: 193177/1610113 (12.0%) reads: 5163638/11769125 (43.9%) Not mapped (no hits)(N): sequences: 757125/1610113 (47.0%) reads: 3700141/11769125 (31.4%) Fri 20 Dec 2024 19:34:11 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/2F1-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: 1809014 # reads with at least one alignment: 1308927 (72.36%) # reads that failed to align: 500087 (27.64%) Reported 6078852 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 538374/1838887 (29.3%) reads: 1154711/10783240 (10.7%) Multi-mapped placed with guidance (P): sequences: 159716/1838887 (8.7%) reads: 777497/10783240 (7.2%) Multi-mapped randomly placed (R): sequences: 160288/1838887 (8.7%) reads: 494873/10783240 (4.6%) Very highly multi-mapped (>=20 hits)(H): sequences: 287945/1838887 (15.7%) reads: 6104139/10783240 (56.6%) Not mapped (no hits)(N): sequences: 692564/1838887 (37.7%) reads: 2252020/10783240 (20.9%) Fri 20 Dec 2024 19:35:25 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/2G1-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: 641997/1809014 (35.5%) reads: 3903179/12374752 (31.5%) Multi-mapped placed with guidance (P): sequences: 325968/1809014 (18.0%) reads: 2428259/12374752 (19.6%) Multi-mapped randomly placed (R): sequences: 205741/1809014 (11.4%) reads: 722026/12374752 (5.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 135221/1809014 (7.5%) reads: 1561549/12374752 (12.6%) Not mapped (no hits)(N): sequences: 500087/1809014 (27.6%) reads: 3759739/12374752 (30.4%) Fri 20 Dec 2024 19:36:25 -0800 PST Merging and indexing alignments Fri 20 Dec 2024 19:40:47 -0800 PST Defining small RNA clusters de novo With 406875252 total reads and mincov of 1 reads per million, the min read depth is 407 Fri 20 Dec 2024 19:41:37 -0800 PST Analyzing cluster properties using 40 threads # reads processed: 49415 # reads with at least one alignment: 143 (0.29%) # reads that failed to align: 49272 (99.71%) Reported 1613 alignments [bam_sort_core] merging from 0 files and 40 in-memory blocks... Fri 20 Dec 2024 19:42:58 -0800 PST Completed Fri 20 Dec 2024 19:42:58 -0800 PST 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 Fri 20 Dec 2024 19:43:09 -0800 PST Analyzing cluster properties using 40 threads Fri 20 Dec 2024 19:43:09 -0800 PST Completed Writing final files Found a total of 51 MIRNA loci Non-MIRNA loci by DicerCall: N 18768 23 25 22 21 24 12 21 8 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 Fri 20 Dec 2024 19:43:23 -0800 PST Run Completed! real 70m35.956s user 829m16.281s sys 269m7.808s