# reads processed: 12209385 # reads with at least one alignment: 7770144 (63.64%) # reads that failed to align: 4439241 (36.36%) Reported 39568567 alignments ShortStack version 4.0.3 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_01/sam/gitrepos/deep-dive/F-Pmea/data/Pocillopora_meandrina_HIv1.assembly.fa', 'known_miRNAs': '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/mirbase-mature-v22.1.fa', 'locifile': None, 'locus': None, 'mincov': 1, 'mmap': 'u', 'nohp': False, 'outdir': '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz'], 'show_secondaries': False, 'strand_cutoff': 0.8, 'threads': 46} Required executable RNAfold : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/RNAfold Required executable strucVis : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/strucVis Required executable bowtie : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/bowtie Required executable bowtie-build : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/bowtie-build Required executable ShortTracks : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/ShortTracks Required executable wigToBigWig : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/wigToBigWig Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/samtools Fri 16 Feb 2024 10:31:22 -0800 PST Required bowtie indices not found. Building them ... Completed Beginning alignment phase Fri 16 Feb 2024 10:35:43 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 13 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 14848953 # reads with at least one alignment: 9561271 (64.39%) # reads that failed to align: 5287682 (35.61%) Reported 43777557 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2133823/12209385 (17.5%) Multi-mapped reads placed (P) with guidance: 3593492/12209385 (29.4%) Multi-mapped reads randomly (R) placed: 1945356/12209385 (15.9%) Very highly (H) multi-mapped reads (>=50 hits): 97473/12209385 (0.8%) Not mapped (N) reads (no hits): 4439241/12209385 (36.4%) Fri 16 Feb 2024 10:41:28 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 15 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 12625701 # reads with at least one alignment: 7270826 (57.59%) # reads that failed to align: 5354875 (42.41%) Reported 37364807 alignments Converting to sorted bam format Uniquely mapped (U) reads: 1899373/14848953 (12.8%) Multi-mapped reads placed (P) with guidance: 5232545/14848953 (35.2%) Multi-mapped reads randomly (R) placed: 2322738/14848953 (15.6%) Very highly (H) multi-mapped reads (>=50 hits): 106615/14848953 (0.7%) Not mapped (N) reads (no hits): 5287682/14848953 (35.6%) Fri 16 Feb 2024 10:47:44 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 13 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 16831731 # reads with at least one alignment: 12867279 (76.45%) # reads that failed to align: 3964452 (23.55%) Reported 51533602 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2021257/12625701 (16.0%) Multi-mapped reads placed (P) with guidance: 3576274/12625701 (28.3%) Multi-mapped reads randomly (R) placed: 1559388/12625701 (12.4%) Very highly (H) multi-mapped reads (>=50 hits): 113907/12625701 (0.9%) Not mapped (N) reads (no hits): 5354875/12625701 (42.4%) Fri 16 Feb 2024 10:53:09 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 17 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 16502248 # reads with at least one alignment: 14062854 (85.22%) # reads that failed to align: 2439394 (14.78%) Reported 53449399 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2930776/16831731 (17.4%) Multi-mapped reads placed (P) with guidance: 5525433/16831731 (32.8%) Multi-mapped reads randomly (R) placed: 4279720/16831731 (25.4%) Very highly (H) multi-mapped reads (>=50 hits): 131350/16831731 (0.8%) Not mapped (N) reads (no hits): 3964452/16831731 (23.6%) Fri 16 Feb 2024 11:00:19 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 17 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... ShortTracks version 1.1 Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/samtools Required executable wigToBigWig : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/wigToBigWig Preparing commands, counting overall reads Getting raw depths samtools view -F 256 -r sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt samtools view -F 256 -r sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt samtools view -F 256 -r sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt samtools view -F 256 -r sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt samtools view -F 256 -r sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt Writing wiggle files /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw ShortTracks version 1.1 Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/samtools Required executable wigToBigWig : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/wigToBigWig Preparing commands, counting overall reads Getting raw depths samtools view -F 272 -e "qlen==21" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_p_depths.txt samtools view -F 256 -f 16 -e "qlen==21" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_m_depths.txt samtools view -F 272 -e "qlen==22" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_p_depths.txt samtools view -F 256 -f 16 -e "qlen==22" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_m_depths.txt samtools view -F 272 -e "qlen==23 || qlen==24" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_p_depths.txt samtools view -F 256 -f 16 -e "qlen==23 || qlen==24" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_m_depths.txt samtools view -F 272 -e "qlen < 21 || qlen > 24" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_p_depths.txt samtools view -F 256 -f 16 -e "qlen < 21 || qlen > 24" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_m_depths.txt Writing wiggle files /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_m.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1-Pmea-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_m.bw Converting to sorted bam format Uniquely mapped (U) reads: 2627232/16502248 (15.9%) Multi-mapped reads placed (P) with guidance: 7239113/16502248 (43.9%) Multi-mapped reads randomly (R) placed: 4025353/16502248 (24.4%) Very highly (H) multi-mapped reads (>=50 hits): 171156/16502248 (1.0%) Not mapped (N) reads (no hits): 2439394/16502248 (14.8%) Fri 16 Feb 2024 11:07:46 -0800 PST Merging and indexing alignments Creating browser tracks by readgroup using ShortTracks Creating browser tracks by readlength and strand using ShortTracks Fri 16 Feb 2024 11:22:13 -0800 PST Defining small RNA clusters de novo With 73018018 total reads and mincov of 1 reads per million, the min read depth is 73 Fri 16 Feb 2024 11:22:35 -0800 PST Analyzing cluster properties using 46 threads # reads processed: 48885 # reads with at least one alignment: 111 (0.23%) # reads that failed to align: 48774 (99.77%) Reported 1714 alignments [bam_sort_core] merging from 0 files and 46 in-memory blocks... Fri 16 Feb 2024 11:24:32 -0800 PST Completed Fri 16 Feb 2024 11:24:32 -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 16 Feb 2024 11:25:09 -0800 PST Analyzing cluster properties using 46 threads Fri 16 Feb 2024 11:25:14 -0800 PST Completed Writing final files Found a total of 35 MIRNA loci Non-MIRNA loci by DicerCall: N 7698 22 33 23 32 24 14 21 11 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 16 Feb 2024 11:25:38 -0800 PST Run Completed! real 54m16.865s user 1086m20.043s sys 324m13.979s