# reads processed: 3598812 # reads with at least one alignment: 2429499 (67.51%) # reads that failed to align: 1169313 (32.49%) Reported 9629194 alignments ShortStack version 4.1.1 Beginning run Options: { 'adapter': None, 'align_only': False, 'autotrim': False, 'autotrim_key': 'TCGGACCAGGCTTCATTCCCC', 'autotrim_only': False, 'bamfile': None, 'dicermax': 24, 'dicermin': 21, 'dn_mirna': True, 'genomefile': '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/data/genome_files/GCF_026571515.1_ASM2657151v2_genomic.fa', 'known_miRNAs': '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/data/mirbase-mature-v22.1.fa', 'locifile': None, 'locus': None, 'make_bigwigs': False, 'mincov': 1, 'mmap': 'u', 'nohp': False, 'outdir': '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/196-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/199-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/211-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/24-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/260-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/26-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/30-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/310-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/33-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/341-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/34-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/35-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/363-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/367-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/376-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/460-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/485-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/501-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/71-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/01.00-trimming-fastp-fastqc/88-fastp-adapters-polyG-31bp-merged.fq.gz'], 'strand_cutoff': 0.8, 'threads': 40} Required executable RNAfold : /home/sam/programs/mambaforge/envs/ShortStack-4.1.1_env/bin/RNAfold Required executable strucVis : /home/sam/programs/mambaforge/envs/ShortStack-4.1.1_env/bin/strucVis Required executable bowtie : /home/sam/programs/mambaforge/envs/ShortStack-4.1.1_env/bin/bowtie Required executable bowtie-build : /home/sam/programs/mambaforge/envs/ShortStack-4.1.1_env/bin/bowtie-build Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack-4.1.1_env/bin/samtools Tue 10 Dec 2024 07:44:44 -0800 PST Condensing reads Beginning alignment phase Tue 10 Dec 2024 08:04:20 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/196-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: 2723627 # reads with at least one alignment: 1862411 (68.38%) # reads that failed to align: 861216 (31.62%) Reported 7100239 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1108950/3598812 (30.8%) reads: 5738230/16412840 (35.0%) Multi-mapped placed with guidance (P): sequences: 766366/3598812 (21.3%) reads: 5347196/16412840 (32.6%) Multi-mapped randomly placed (R): sequences: 418999/3598812 (11.6%) reads: 1460128/16412840 (8.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 135184/3598812 (3.8%) reads: 495285/16412840 (3.0%) Not mapped (no hits)(N): sequences: 1169313/3598812 (32.5%) reads: 3372001/16412840 (20.5%) Tue 10 Dec 2024 08:05:48 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/199-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: 3216924 # reads with at least one alignment: 2234376 (69.46%) # reads that failed to align: 982548 (30.54%) Reported 9102819 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 861824/2723627 (31.6%) reads: 4921767/13501046 (36.5%) Multi-mapped placed with guidance (P): sequences: 568965/2723627 (20.9%) reads: 4221296/13501046 (31.3%) Multi-mapped randomly placed (R): sequences: 338260/2723627 (12.4%) reads: 1186914/13501046 (8.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 93362/2723627 (3.4%) reads: 379100/13501046 (2.8%) Not mapped (no hits)(N): sequences: 861216/2723627 (31.6%) reads: 2791969/13501046 (20.7%) Tue 10 Dec 2024 08:06:48 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/211-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: 3004124 # reads with at least one alignment: 2104498 (70.05%) # reads that failed to align: 899626 (29.95%) Reported 9138190 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1006657/3216924 (31.3%) reads: 5150058/14331623 (35.9%) Multi-mapped placed with guidance (P): sequences: 705165/3216924 (21.9%) reads: 4545103/14331623 (31.7%) Multi-mapped randomly placed (R): sequences: 391340/3216924 (12.2%) reads: 1329318/14331623 (9.3%) Very highly multi-mapped (>=20 hits)(H): sequences: 131214/3216924 (4.1%) reads: 496398/14331623 (3.5%) Not mapped (no hits)(N): sequences: 982548/3216924 (30.5%) reads: 2810746/14331623 (19.6%) Tue 10 Dec 2024 08:07:57 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/24-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: 2938915 # reads with at least one alignment: 2058288 (70.04%) # reads that failed to align: 880627 (29.96%) Reported 8591372 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 900075/3004124 (30.0%) reads: 5404207/15464708 (34.9%) Multi-mapped placed with guidance (P): sequences: 660277/3004124 (22.0%) reads: 4855540/15464708 (31.4%) Multi-mapped randomly placed (R): sequences: 403979/3004124 (13.4%) reads: 1564897/15464708 (10.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 140167/3004124 (4.7%) reads: 591650/15464708 (3.8%) Not mapped (no hits)(N): sequences: 899626/3004124 (29.9%) reads: 3048414/15464708 (19.7%) Tue 10 Dec 2024 08:09:16 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/260-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: 2521265 # reads with at least one alignment: 1736670 (68.88%) # reads that failed to align: 784595 (31.12%) Reported 7142746 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 905898/2938915 (30.8%) reads: 5685238/15809613 (36.0%) Multi-mapped placed with guidance (P): sequences: 630090/2938915 (21.4%) reads: 4929476/15809613 (31.2%) Multi-mapped randomly placed (R): sequences: 396349/2938915 (13.5%) reads: 1633867/15809613 (10.3%) Very highly multi-mapped (>=20 hits)(H): sequences: 125951/2938915 (4.3%) reads: 561421/15809613 (3.6%) Not mapped (no hits)(N): sequences: 880627/2938915 (30.0%) reads: 2999611/15809613 (19.0%) Tue 10 Dec 2024 08:10:37 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/26-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: 3157152 # reads with at least one alignment: 2197023 (69.59%) # reads that failed to align: 960129 (30.41%) Reported 8910059 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 770434/2521265 (30.6%) reads: 5287297/14609516 (36.2%) Multi-mapped placed with guidance (P): sequences: 529754/2521265 (21.0%) reads: 4373850/14609516 (29.9%) Multi-mapped randomly placed (R): sequences: 333211/2521265 (13.2%) reads: 1478278/14609516 (10.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 103271/2521265 (4.1%) reads: 450973/14609516 (3.1%) Not mapped (no hits)(N): sequences: 784595/2521265 (31.1%) reads: 3019118/14609516 (20.7%) Tue 10 Dec 2024 08:11:36 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/30-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: 2951065 # reads with at least one alignment: 2079245 (70.46%) # reads that failed to align: 871820 (29.54%) Reported 8582048 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 971593/3157152 (30.8%) reads: 5640325/16076914 (35.1%) Multi-mapped placed with guidance (P): sequences: 723289/3157152 (22.9%) reads: 5428134/16076914 (33.8%) Multi-mapped randomly placed (R): sequences: 378151/3157152 (12.0%) reads: 1411907/16076914 (8.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 123990/3157152 (3.9%) reads: 509091/16076914 (3.2%) Not mapped (no hits)(N): sequences: 960129/3157152 (30.4%) reads: 3087457/16076914 (19.2%) Tue 10 Dec 2024 08:12:54 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/310-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: 3052106 # reads with at least one alignment: 2119160 (69.43%) # reads that failed to align: 932946 (30.57%) Reported 8751476 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 919231/2951065 (31.1%) reads: 5685039/15957699 (35.6%) Multi-mapped placed with guidance (P): sequences: 654368/2951065 (22.2%) reads: 5326891/15957699 (33.4%) Multi-mapped randomly placed (R): sequences: 380272/2951065 (12.9%) reads: 1503718/15957699 (9.4%) Very highly multi-mapped (>=20 hits)(H): sequences: 125374/2951065 (4.2%) reads: 562715/15957699 (3.5%) Not mapped (no hits)(N): sequences: 871820/2951065 (29.5%) reads: 2879336/15957699 (18.0%) Tue 10 Dec 2024 08:14:02 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/33-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: 2824599 # reads with at least one alignment: 2004392 (70.96%) # reads that failed to align: 820207 (29.04%) Reported 8594443 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 948182/3052106 (31.1%) reads: 5806018/16654516 (34.9%) Multi-mapped placed with guidance (P): sequences: 666092/3052106 (21.8%) reads: 5510171/16654516 (33.1%) Multi-mapped randomly placed (R): sequences: 374440/3052106 (12.3%) reads: 1645934/16654516 (9.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 130446/3052106 (4.3%) reads: 591339/16654516 (3.6%) Not mapped (no hits)(N): sequences: 932946/3052106 (30.6%) reads: 3101054/16654516 (18.6%) Tue 10 Dec 2024 08:15:18 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/341-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: 3373653 # reads with at least one alignment: 2341704 (69.41%) # reads that failed to align: 1031949 (30.59%) Reported 9261154 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 859708/2824599 (30.4%) reads: 5423419/15703770 (34.5%) Multi-mapped placed with guidance (P): sequences: 629602/2824599 (22.3%) reads: 4882493/15703770 (31.1%) Multi-mapped randomly placed (R): sequences: 386229/2824599 (13.7%) reads: 1734657/15703770 (11.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 128853/2824599 (4.6%) reads: 614343/15703770 (3.9%) Not mapped (no hits)(N): sequences: 820207/2824599 (29.0%) reads: 3048858/15703770 (19.4%) Tue 10 Dec 2024 08:16:32 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/34-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: 2682130 # reads with at least one alignment: 1829283 (68.20%) # reads that failed to align: 852847 (31.80%) Reported 7506414 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1054451/3373653 (31.3%) reads: 7018684/18959577 (37.0%) Multi-mapped placed with guidance (P): sequences: 750429/3373653 (22.2%) reads: 5758705/18959577 (30.4%) Multi-mapped randomly placed (R): sequences: 415513/3373653 (12.3%) reads: 1924747/18959577 (10.2%) Very highly multi-mapped (>=20 hits)(H): sequences: 121311/3373653 (3.6%) reads: 543368/18959577 (2.9%) Not mapped (no hits)(N): sequences: 1031949/3373653 (30.6%) reads: 3714073/18959577 (19.6%) Tue 10 Dec 2024 08:17:52 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/35-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: 2871340 # reads with at least one alignment: 1997649 (69.57%) # reads that failed to align: 873691 (30.43%) Reported 8057045 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 812433/2682130 (30.3%) reads: 5211636/14222039 (36.6%) Multi-mapped placed with guidance (P): sequences: 562802/2682130 (21.0%) reads: 4290462/14222039 (30.2%) Multi-mapped randomly placed (R): sequences: 346381/2682130 (12.9%) reads: 1429036/14222039 (10.0%) Very highly multi-mapped (>=20 hits)(H): sequences: 107667/2682130 (4.0%) reads: 484955/14222039 (3.4%) Not mapped (no hits)(N): sequences: 852847/2682130 (31.8%) reads: 2805950/14222039 (19.7%) Tue 10 Dec 2024 08:19:02 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/363-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: 3065997 # reads with at least one alignment: 2163860 (70.58%) # reads that failed to align: 902137 (29.42%) Reported 9335108 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 899467/2871340 (31.3%) reads: 6184248/17268543 (35.8%) Multi-mapped placed with guidance (P): sequences: 621797/2871340 (21.7%) reads: 5620155/17268543 (32.5%) Multi-mapped randomly placed (R): sequences: 364872/2871340 (12.7%) reads: 1712497/17268543 (9.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 111513/2871340 (3.9%) reads: 529612/17268543 (3.1%) Not mapped (no hits)(N): sequences: 873691/2871340 (30.4%) reads: 3222031/17268543 (18.7%) Tue 10 Dec 2024 08:20:14 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/367-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: 4504581 # reads with at least one alignment: 3095877 (68.73%) # reads that failed to align: 1408704 (31.27%) Reported 12393101 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 933180/3065997 (30.4%) reads: 5502263/15680761 (35.1%) Multi-mapped placed with guidance (P): sequences: 688353/3065997 (22.5%) reads: 5087545/15680761 (32.4%) Multi-mapped randomly placed (R): sequences: 401177/3065997 (13.1%) reads: 1578755/15680761 (10.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 141150/3065997 (4.6%) reads: 554667/15680761 (3.5%) Not mapped (no hits)(N): sequences: 902137/3065997 (29.4%) reads: 2957531/15680761 (18.9%) Tue 10 Dec 2024 08:21:32 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/376-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: 3060928 # reads with at least one alignment: 2089172 (68.25%) # reads that failed to align: 971756 (31.75%) Reported 8483476 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1381652/4504581 (30.7%) reads: 10778375/29730374 (36.3%) Multi-mapped placed with guidance (P): sequences: 1056376/4504581 (23.5%) reads: 9375217/29730374 (31.5%) Multi-mapped randomly placed (R): sequences: 488683/4504581 (10.8%) reads: 2330402/29730374 (7.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 169166/4504581 (3.8%) reads: 1238612/29730374 (4.2%) Not mapped (no hits)(N): sequences: 1408704/4504581 (31.3%) reads: 6007768/29730374 (20.2%) Tue 10 Dec 2024 08:23:02 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/460-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: 3024117 # reads with at least one alignment: 2111801 (69.83%) # reads that failed to align: 912316 (30.17%) Reported 8564690 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 954008/3060928 (31.2%) reads: 5376280/14767899 (36.4%) Multi-mapped placed with guidance (P): sequences: 635455/3060928 (20.8%) reads: 4401137/14767899 (29.8%) Multi-mapped randomly placed (R): sequences: 374775/3060928 (12.2%) reads: 1295871/14767899 (8.8%) Very highly multi-mapped (>=20 hits)(H): sequences: 124934/3060928 (4.1%) reads: 507564/14767899 (3.4%) Not mapped (no hits)(N): sequences: 971756/3060928 (31.7%) reads: 3187047/14767899 (21.6%) Tue 10 Dec 2024 08:24:15 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/485-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: 3574175 # reads with at least one alignment: 2481529 (69.43%) # reads that failed to align: 1092646 (30.57%) Reported 10574957 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 945245/3024117 (31.3%) reads: 5525495/15645649 (35.3%) Multi-mapped placed with guidance (P): sequences: 666256/3024117 (22.0%) reads: 5102646/15645649 (32.6%) Multi-mapped randomly placed (R): sequences: 379132/3024117 (12.5%) reads: 1430133/15645649 (9.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 121168/3024117 (4.0%) reads: 491802/15645649 (3.1%) Not mapped (no hits)(N): sequences: 912316/3024117 (30.2%) reads: 3095573/15645649 (19.8%) Tue 10 Dec 2024 08:25:23 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/501-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: 4368376 # reads with at least one alignment: 2877882 (65.88%) # reads that failed to align: 1490494 (34.12%) Reported 13016301 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1089499/3574175 (30.5%) reads: 6235317/17161714 (36.3%) Multi-mapped placed with guidance (P): sequences: 796338/3574175 (22.3%) reads: 5272243/17161714 (30.7%) Multi-mapped randomly placed (R): sequences: 431289/3574175 (12.1%) reads: 1532386/17161714 (8.9%) Very highly multi-mapped (>=20 hits)(H): sequences: 164403/3574175 (4.6%) reads: 704647/17161714 (4.1%) Not mapped (no hits)(N): sequences: 1092646/3574175 (30.6%) reads: 3417121/17161714 (19.9%) Tue 10 Dec 2024 08:26:45 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/71-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: 3373635 # reads with at least one alignment: 2167948 (64.26%) # reads that failed to align: 1205687 (35.74%) Reported 9080512 alignments Converting to sorted bam format Uniquely mapped (U): sequences: 1264120/4368376 (28.9%) reads: 6496868/18881184 (34.4%) Multi-mapped placed with guidance (P): sequences: 920721/4368376 (21.1%) reads: 5142586/18881184 (27.2%) Multi-mapped randomly placed (R): sequences: 454224/4368376 (10.4%) reads: 1532582/18881184 (8.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 238817/4368376 (5.5%) reads: 1308637/18881184 (6.9%) Not mapped (no hits)(N): sequences: 1490494/4368376 (34.1%) reads: 4400511/18881184 (23.3%) Tue 10 Dec 2024 08:28:27 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/RobertsLab/project-clam-oa/output/02.00-ShortStack-31bp-fastp-merged/ShortStack_out/88-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... Converting to sorted bam format Uniquely mapped (U): sequences: 940864/3373635 (27.9%) reads: 6178572/18003539 (34.3%) Multi-mapped placed with guidance (P): sequences: 691468/3373635 (20.5%) reads: 5475445/18003539 (30.4%) Multi-mapped randomly placed (R): sequences: 405508/3373635 (12.0%) reads: 1633850/18003539 (9.1%) Very highly multi-mapped (>=20 hits)(H): sequences: 130108/3373635 (3.9%) reads: 574538/18003539 (3.2%) Not mapped (no hits)(N): sequences: 1205687/3373635 (35.7%) reads: 4141134/18003539 (23.0%) Tue 10 Dec 2024 08:29:49 -0800 PST Merging and indexing alignments Tue 10 Dec 2024 08:33:26 -0800 PST Defining small RNA clusters de novo With 334843524 total reads and mincov of 1 reads per million, the min read depth is 335 Tue 10 Dec 2024 08:34:15 -0800 PST Analyzing cluster properties using 40 threads # reads processed: 48885 # reads with at least one alignment: 1155 (2.36%) # reads that failed to align: 47730 (97.64%) Reported 24638 alignments [bam_sort_core] merging from 0 files and 40 in-memory blocks... Tue 10 Dec 2024 08:35:31 -0800 PST Completed Tue 10 Dec 2024 08:35:31 -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 Tue 10 Dec 2024 08:36:50 -0800 PST Analyzing cluster properties using 40 threads Tue 10 Dec 2024 08:36:50 -0800 PST Completed Writing final files Found a total of 37 MIRNA loci Non-MIRNA loci by DicerCall: N 33525 22 60 21 18 23 17 24 9 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 Tue 10 Dec 2024 08:37:06 -0800 PST Run Completed! real 52m22.645s user 672m59.895s sys 196m42.848s