# reads processed: 14761972 # reads with at least one alignment: 11338963 (76.81%) # reads that failed to align: 3423009 (23.19%) Reported 46469862 alignments ShortStack version 4.0.2 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/E-Peve/data/Porites_evermanni_v1.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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-73-S1-TP2.flexbar_trim.25bp_1.fastq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-73-S1-TP2.flexbar_trim.25bp_2.fastq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-79-S1-TP2.flexbar_trim.25bp_1.fastq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-79-S1-TP2.flexbar_trim.25bp_2.fastq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-82-S1-TP2.flexbar_trim.25bp_1.fastq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-82-S1-TP2.flexbar_trim.25bp_2.fastq.gz'], 'show_secondaries': False, 'strand_cutoff': 0.8, 'threads': 46} Required executable RNAfold : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/RNAfold Required executable strucVis : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/strucVis Required executable bowtie : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/bowtie Required executable bowtie-build : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/bowtie-build Required executable ShortTracks : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/ShortTracks Required executable wigToBigWig : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/wigToBigWig Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/samtools Beginning alignment phase Fri 22 Mar 2024 10:15:17 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-73-S1-TP2.flexbar_trim.25bp_1.fastq.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: 14761972 # reads with at least one alignment: 10676912 (72.33%) # reads that failed to align: 4085060 (27.67%) Reported 45431393 alignments Converting to sorted bam format Uniquely mapped (U) reads: 5128658/14761972 (34.7%) Multi-mapped reads placed (P) with guidance: 3322372/14761972 (22.5%) Multi-mapped reads randomly (R) placed: 2783746/14761972 (18.9%) Very highly (H) multi-mapped reads (>=50 hits): 104187/14761972 (0.7%) Not mapped (N) reads (no hits): 3423009/14761972 (23.2%) Fri 22 Mar 2024 10:19:34 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-73-S1-TP2.flexbar_trim.25bp_2.fastq.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: 15794990 # reads with at least one alignment: 13071724 (82.76%) # reads that failed to align: 2723266 (17.24%) Reported 82400372 alignments Converting to sorted bam format Uniquely mapped (U) reads: 4451682/14761972 (30.2%) Multi-mapped reads placed (P) with guidance: 3361569/14761972 (22.8%) Multi-mapped reads randomly (R) placed: 2751737/14761972 (18.6%) Very highly (H) multi-mapped reads (>=50 hits): 111924/14761972 (0.8%) Not mapped (N) reads (no hits): 4085060/14761972 (27.7%) Fri 22 Mar 2024 10:23:44 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-79-S1-TP2.flexbar_trim.25bp_1.fastq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 16 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 15794990 # reads with at least one alignment: 12515143 (79.23%) # reads that failed to align: 3279847 (20.77%) Reported 86911473 alignments Converting to sorted bam format Uniquely mapped (U) reads: 6569881/15794990 (41.6%) Multi-mapped reads placed (P) with guidance: 5108619/15794990 (32.3%) Multi-mapped reads randomly (R) placed: 1265732/15794990 (8.0%) Very highly (H) multi-mapped reads (>=50 hits): 127492/15794990 (0.8%) Not mapped (N) reads (no hits): 2723266/15794990 (17.2%) Fri 22 Mar 2024 10:30:38 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-79-S1-TP2.flexbar_trim.25bp_2.fastq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 16 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 17260661 # reads with at least one alignment: 14539970 (84.24%) # reads that failed to align: 2720691 (15.76%) Reported 77796611 alignments Converting to sorted bam format Uniquely mapped (U) reads: 5864191/15794990 (37.1%) Multi-mapped reads placed (P) with guidance: 5286894/15794990 (33.5%) Multi-mapped reads randomly (R) placed: 1228313/15794990 (7.8%) Very highly (H) multi-mapped reads (>=50 hits): 135745/15794990 (0.9%) Not mapped (N) reads (no hits): 3279847/15794990 (20.8%) Fri 22 Mar 2024 10:37:59 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-82-S1-TP2.flexbar_trim.25bp_1.fastq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 18 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 17260661 # reads with at least one alignment: 14061472 (81.47%) # reads that failed to align: 3199189 (18.53%) Reported 83067454 alignments Converting to sorted bam format Uniquely mapped (U) reads: 8038531/17260661 (46.6%) Multi-mapped reads placed (P) with guidance: 4789607/17260661 (27.7%) Multi-mapped reads randomly (R) placed: 1579338/17260661 (9.1%) Very highly (H) multi-mapped reads (>=50 hits): 132494/17260661 (0.8%) Not mapped (N) reads (no hits): 2720691/17260661 (15.8%) Fri 22 Mar 2024 10:44:38 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/06-Peve-sRNAseq-trimming/trimmed-reads/sRNA-POR-82-S1-TP2.flexbar_trim.25bp_2.fastq.gz First pass alignment with bowtie using 46 threads Second pass - placing multimappers using 46 threads to process 18 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/ShortStack4_env/bin/samtools Required executable wigToBigWig : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/wigToBigWig Preparing commands, counting overall reads Getting raw depths samtools view -F 256 -r sRNA-POR-73-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-73-S1-TP2.flexbar_trim.25bp_1_depths.txt samtools view -F 256 -r sRNA-POR-73-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-73-S1-TP2.flexbar_trim.25bp_2_depths.txt samtools view -F 256 -r sRNA-POR-79-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-79-S1-TP2.flexbar_trim.25bp_1_depths.txt samtools view -F 256 -r sRNA-POR-79-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-79-S1-TP2.flexbar_trim.25bp_2_depths.txt samtools view -F 256 -r sRNA-POR-82-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-82-S1-TP2.flexbar_trim.25bp_1_depths.txt samtools view -F 256 -r sRNA-POR-82-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-82-S1-TP2.flexbar_trim.25bp_2_depths.txt Writing wiggle files /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-73-S1-TP2.flexbar_trim.25bp_1.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-73-S1-TP2.flexbar_trim.25bp_2.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-79-S1-TP2.flexbar_trim.25bp_1.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-79-S1-TP2.flexbar_trim.25bp_2.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-82-S1-TP2.flexbar_trim.25bp_1.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-82-S1-TP2.flexbar_trim.25bp_2.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-73-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-73-S1-TP2.flexbar_trim.25bp_1.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-73-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-73-S1-TP2.flexbar_trim.25bp_2.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-79-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-79-S1-TP2.flexbar_trim.25bp_1.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-79-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-79-S1-TP2.flexbar_trim.25bp_2.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-82-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-82-S1-TP2.flexbar_trim.25bp_1.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-82-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POR-82-S1-TP2.flexbar_trim.25bp_2.bw ShortTracks version 1.1 Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/samtools Required executable wigToBigWig : /home/sam/programs/mambaforge/envs/ShortStack4_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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/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/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m_depths.txt Writing wiggle files /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/08-Peve-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.bw Converting to sorted bam format Uniquely mapped (U) reads: 7347539/17260661 (42.6%) Multi-mapped reads placed (P) with guidance: 5044111/17260661 (29.2%) Multi-mapped reads randomly (R) placed: 1536225/17260661 (8.9%) Very highly (H) multi-mapped reads (>=50 hits): 133597/17260661 (0.8%) Not mapped (N) reads (no hits): 3199189/17260661 (18.5%) Fri 22 Mar 2024 10:51:43 -0700 PDT Merging and indexing alignments Creating browser tracks by readgroup using ShortTracks Creating browser tracks by readlength and strand using ShortTracks Fri 22 Mar 2024 11:09:43 -0700 PDT Defining small RNA clusters de novo With 95635246 total reads and mincov of 1 reads per million, the min read depth is 96 Fri 22 Mar 2024 11:10:07 -0700 PDT Analyzing cluster properties using 46 threads # reads processed: 48885 # reads with at least one alignment: 84 (0.17%) # reads that failed to align: 48801 (99.83%) Reported 2502 alignments [bam_sort_core] merging from 0 files and 46 in-memory blocks... Fri 22 Mar 2024 11:11:22 -0700 PDT Completed Fri 22 Mar 2024 11:11:22 -0700 PDT Searching for valid microRNA loci Aligning known_miRNAs sequences to genome Screening of possible microRNAs from user provided known_miRNAs Screening of possible de novo microRNAs No microRNA loci were found! Writing final files Non-MIRNA loci by DicerCall: N 14887 22 55 23 42 21 25 24 24 Fri 22 Mar 2024 11:11:43 -0700 PDT Run Completed! real 56m25.877s user 1149m4.970s sys 389m46.753s