# reads processed: 15287011 # reads with at least one alignment: 10779985 (70.52%) # reads that failed to align: 4507026 (29.48%) Reported 67685588 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/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-140-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-145-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-150-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-173-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-178-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz'], 'show_secondaries': False, 'strand_cutoff': 0.8, 'threads': 40} 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 Beginning alignment phase Wed 14 Feb 2024 15:26:09 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-140-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 16 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 17548180 # reads with at least one alignment: 12620567 (71.92%) # reads that failed to align: 4927613 (28.08%) Reported 87451104 alignments Converting to sorted bam format Uniquely mapped (U) reads: 3645730/15287011 (23.8%) Multi-mapped reads placed (P) with guidance: 5407562/15287011 (35.4%) Multi-mapped reads randomly (R) placed: 1464223/15287011 (9.6%) Very highly (H) multi-mapped reads (>=50 hits): 262470/15287011 (1.7%) Not mapped (N) reads (no hits): 4507026/15287011 (29.5%) Wed 14 Feb 2024 15:32:11 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-145-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 18 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 18647411 # reads with at least one alignment: 12711274 (68.17%) # reads that failed to align: 5936137 (31.83%) Reported 77302090 alignments Converting to sorted bam format Uniquely mapped (U) reads: 3978703/17548180 (22.7%) Multi-mapped reads placed (P) with guidance: 6731792/17548180 (38.4%) Multi-mapped reads randomly (R) placed: 1532996/17548180 (8.7%) Very highly (H) multi-mapped reads (>=50 hits): 377076/17548180 (2.1%) Not mapped (N) reads (no hits): 4927613/17548180 (28.1%) Wed 14 Feb 2024 15:39:44 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-150-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 19 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 16583674 # reads with at least one alignment: 11656481 (70.29%) # reads that failed to align: 4927193 (29.71%) Reported 75780970 alignments Converting to sorted bam format Uniquely mapped (U) reads: 4822000/18647411 (25.9%) Multi-mapped reads placed (P) with guidance: 6074952/18647411 (32.6%) Multi-mapped reads randomly (R) placed: 1486739/18647411 (8.0%) Very highly (H) multi-mapped reads (>=50 hits): 327583/18647411 (1.8%) Not mapped (N) reads (no hits): 5936137/18647411 (31.8%) Wed 14 Feb 2024 15:46:45 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-173-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 17 chunks [bam_sort_core] merging from 0 files and 40 in-memory blocks... # reads processed: 14608168 # reads with at least one alignment: 10284854 (70.40%) # reads that failed to align: 4323314 (29.60%) Reported 71296730 alignments Converting to sorted bam format Uniquely mapped (U) reads: 3771097/16583674 (22.7%) Multi-mapped reads placed (P) with guidance: 6155877/16583674 (37.1%) Multi-mapped reads randomly (R) placed: 1451206/16583674 (8.8%) Very highly (H) multi-mapped reads (>=50 hits): 278301/16583674 (1.7%) Not mapped (N) reads (no hits): 4927193/16583674 (29.7%) Wed 14 Feb 2024 15:53:31 -0800 PST Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.1-Dapul-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-ACR-178-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz First pass alignment with bowtie using 40 threads Second pass - placing multimappers using 40 threads to process 15 chunks [bam_sort_core] merging from 0 files and 40 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-ACR-140-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt samtools view -F 256 -r sRNA-ACR-145-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt samtools view -F 256 -r sRNA-ACR-150-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt samtools view -F 256 -r sRNA-ACR-173-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt samtools view -F 256 -r sRNA-ACR-178-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt Writing wiggle files /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_sRNA-ACR-178-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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-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/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_m_depths.txt Writing wiggle files /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_m.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_21_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_22_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_23-24_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.1-Apul-sRNAseq-ShortStack-R1-reads/ShortStack_out/merged_alignments_other_m.bw Converting to sorted bam format Uniquely mapped (U) reads: 3295229/14608168 (22.6%) Multi-mapped reads placed (P) with guidance: 5433940/14608168 (37.2%) Multi-mapped reads randomly (R) placed: 1246471/14608168 (8.5%) Very highly (H) multi-mapped reads (>=50 hits): 309214/14608168 (2.1%) Not mapped (N) reads (no hits): 4323314/14608168 (29.6%) Wed 14 Feb 2024 15:59:51 -0800 PST Merging and indexing alignments Creating browser tracks by readgroup using ShortTracks Creating browser tracks by readlength and strand using ShortTracks Wed 14 Feb 2024 16:16:45 -0800 PST Defining small RNA clusters de novo With 82674444 total reads and mincov of 1 reads per million, the min read depth is 83 Wed 14 Feb 2024 16:17:10 -0800 PST Analyzing cluster properties using 40 threads # reads processed: 48885 # reads with at least one alignment: 47 (0.10%) # reads that failed to align: 48838 (99.90%) Reported 1284 alignments [bam_sort_core] merging from 0 files and 40 in-memory blocks... Wed 14 Feb 2024 16:18:06 -0800 PST Completed Wed 14 Feb 2024 16:18:06 -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 Wed 14 Feb 2024 16:18:14 -0800 PST Analyzing cluster properties using 40 threads Warning: the index file is older than the FASTA file. Wed 14 Feb 2024 16:18:20 -0800 PST Completed Writing final files Found a total of 27 MIRNA loci Non-MIRNA loci by DicerCall: N 19203 22 37 23 33 21 9 24 6 Creating visualizations of microRNA loci with strucVis <<< WARNING >>> Do not rely on these results alone to annotate new MIRNA loci! The false positive rate for de novo MIRNA identification is low, but NOT ZERO Insepct each mirna locus, especially the strucVis output, and see https://doi.org/10.1105/tpc.17.00851 , https://doi.org/10.1093/nar/gky1141 Wed 14 Feb 2024 16:18:45 -0800 PST Run Completed! real 52m36.154s user 934m28.985s sys 293m32.838s