# reads processed: 15063975 # reads with at least one alignment: 9782238 (64.94%) # reads that failed to align: 5281737 (35.06%) Reported 55290048 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_02/shedurkin/deep-dive/F-Pmea/data/Pmea/Pocillopora_meandrina_HIv1.assembly.fa', 'known_miRNAs': '/home/shared/8TB_HDD_02/shedurkin/deep-dive/data/mirbase-mature-v22.1.fa', 'locifile': None, 'locus': None, 'mincov': 1, 'mmap': 'u', 'nohp': False, 'outdir': '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-47-S1-TP2.flexbar_trim.25bp_1.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-47-S1-TP2.flexbar_trim.25bp_2.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-48-S1-TP2.flexbar_trim.25bp_1.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-48-S1-TP2.flexbar_trim.25bp_2.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-50-S1-TP2.flexbar_trim.25bp_1.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-50-S1-TP2.flexbar_trim.25bp_2.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-53-S1-TP2.flexbar_trim.25bp_1.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-53-S1-TP2.flexbar_trim.25bp_2.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-57-S1-TP2.flexbar_trim.25bp_1.fastq.gz', '/home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-57-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 Thu 30 Nov 2023 15:50:29 -0800 PST Required bowtie indices not found. Building them ... Completed Beginning alignment phase Thu 30 Nov 2023 15:54:22 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-47-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: 15063975 # reads with at least one alignment: 9604039 (63.76%) # reads that failed to align: 5459936 (36.24%) Reported 51217763 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2277004/15063975 (15.1%) Multi-mapped reads placed (P) with guidance: 5027929/15063975 (33.4%) Multi-mapped reads randomly (R) placed: 2197291/15063975 (14.6%) Very highly (H) multi-mapped reads (>=50 hits): 280014/15063975 (1.9%) Not mapped (N) reads (no hits): 5281737/15063975 (35.1%) Thu 30 Nov 2023 16:01:00 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-47-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: 16574535 # reads with at least one alignment: 10703744 (64.58%) # reads that failed to align: 5870791 (35.42%) Reported 49150938 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2321579/15063975 (15.4%) Multi-mapped reads placed (P) with guidance: 5163916/15063975 (34.3%) Multi-mapped reads randomly (R) placed: 1949275/15063975 (12.9%) Very highly (H) multi-mapped reads (>=50 hits): 169269/15063975 (1.1%) Not mapped (N) reads (no hits): 5459936/15063975 (36.2%) Thu 30 Nov 2023 16:07:03 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-48-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 17 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 16574535 # reads with at least one alignment: 10587953 (63.88%) # reads that failed to align: 5986582 (36.12%) Reported 48347223 alignments Converting to sorted bam format Uniquely mapped (U) reads: 1999451/16574535 (12.1%) Multi-mapped reads placed (P) with guidance: 5904484/16574535 (35.6%) Multi-mapped reads randomly (R) placed: 2680885/16574535 (16.2%) Very highly (H) multi-mapped reads (>=50 hits): 118924/16574535 (0.7%) Not mapped (N) reads (no hits): 5870791/16574535 (35.4%) Thu 30 Nov 2023 16:12:52 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-48-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 17 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 14858812 # reads with at least one alignment: 8787387 (59.14%) # reads that failed to align: 6071425 (40.86%) Reported 44785573 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2001792/16574535 (12.1%) Multi-mapped reads placed (P) with guidance: 5949715/16574535 (35.9%) Multi-mapped reads randomly (R) placed: 2487570/16574535 (15.0%) Very highly (H) multi-mapped reads (>=50 hits): 148876/16574535 (0.9%) Not mapped (N) reads (no hits): 5986582/16574535 (36.1%) Thu 30 Nov 2023 16:18:21 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-50-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: 14858812 # reads with at least one alignment: 8686601 (58.46%) # reads that failed to align: 6172211 (41.54%) Reported 44595699 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2112577/14858812 (14.2%) Multi-mapped reads placed (P) with guidance: 4733749/14858812 (31.9%) Multi-mapped reads randomly (R) placed: 1787501/14858812 (12.0%) Very highly (H) multi-mapped reads (>=50 hits): 153560/14858812 (1.0%) Not mapped (N) reads (no hits): 6071425/14858812 (40.9%) Thu 30 Nov 2023 16:23:28 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-50-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: 18481608 # reads with at least one alignment: 14404188 (77.94%) # reads that failed to align: 4077420 (22.06%) Reported 58140266 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2140008/14858812 (14.4%) Multi-mapped reads placed (P) with guidance: 4715818/14858812 (31.7%) Multi-mapped reads randomly (R) placed: 1658138/14858812 (11.2%) Very highly (H) multi-mapped reads (>=50 hits): 172637/14858812 (1.2%) Not mapped (N) reads (no hits): 6172211/14858812 (41.5%) Thu 30 Nov 2023 16:28:34 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-53-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 19 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 18481608 # reads with at least one alignment: 14111815 (76.36%) # reads that failed to align: 4369793 (23.64%) Reported 56895198 alignments Converting to sorted bam format Uniquely mapped (U) reads: 3272135/18481608 (17.7%) Multi-mapped reads placed (P) with guidance: 6276510/18481608 (34.0%) Multi-mapped reads randomly (R) placed: 4691391/18481608 (25.4%) Very highly (H) multi-mapped reads (>=50 hits): 164152/18481608 (0.9%) Not mapped (N) reads (no hits): 4077420/18481608 (22.1%) Thu 30 Nov 2023 16:34:54 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-53-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 19 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 16574698 # reads with at least one alignment: 13792666 (83.22%) # reads that failed to align: 2782032 (16.78%) Reported 49700739 alignments Converting to sorted bam format Uniquely mapped (U) reads: 3222983/18481608 (17.4%) Multi-mapped reads placed (P) with guidance: 6189165/18481608 (33.5%) Multi-mapped reads randomly (R) placed: 4518740/18481608 (24.4%) Very highly (H) multi-mapped reads (>=50 hits): 180927/18481608 (1.0%) Not mapped (N) reads (no hits): 4369793/18481608 (23.6%) Thu 30 Nov 2023 16:41:18 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-57-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 17 chunks [bam_sort_core] merging from 0 files and 46 in-memory blocks... # reads processed: 16574698 # reads with at least one alignment: 13637176 (82.28%) # reads that failed to align: 2937522 (17.72%) Reported 50261555 alignments Converting to sorted bam format Uniquely mapped (U) reads: 2712534/16574698 (16.4%) Multi-mapped reads placed (P) with guidance: 6640321/16574698 (40.1%) Multi-mapped reads randomly (R) placed: 4298012/16574698 (25.9%) Very highly (H) multi-mapped reads (>=50 hits): 141799/16574698 (0.9%) Not mapped (N) reads (no hits): 2782032/16574698 (16.8%) Thu 30 Nov 2023 16:46:58 -0800 PST Aligning /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/08-Pmea-sRNAseq-trimming/trimmed-reads/sRNA-POC-57-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 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/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-POC-47-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2.flexbar_trim.25bp_1_depths.txt samtools view -F 256 -r sRNA-POC-47-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2.flexbar_trim.25bp_2_depths.txt samtools view -F 256 -r sRNA-POC-48-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2.flexbar_trim.25bp_1_depths.txt samtools view -F 256 -r sRNA-POC-48-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2.flexbar_trim.25bp_2_depths.txt samtools view -F 256 -r sRNA-POC-50-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2.flexbar_trim.25bp_1_depths.txt samtools view -F 256 -r sRNA-POC-50-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2.flexbar_trim.25bp_2_depths.txt samtools view -F 256 -r sRNA-POC-53-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2.flexbar_trim.25bp_1_depths.txt samtools view -F 256 -r sRNA-POC-53-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2.flexbar_trim.25bp_2_depths.txt samtools view -F 256 -r sRNA-POC-57-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2.flexbar_trim.25bp_1_depths.txt samtools view -F 256 -r sRNA-POC-57-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2.flexbar_trim.25bp_2_depths.txt Writing wiggle files /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2.flexbar_trim.25bp_1.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2.flexbar_trim.25bp_2.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2.flexbar_trim.25bp_1.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2.flexbar_trim.25bp_2.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2.flexbar_trim.25bp_1.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2.flexbar_trim.25bp_2.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2.flexbar_trim.25bp_1.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2.flexbar_trim.25bp_2.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2.flexbar_trim.25bp_1.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2.flexbar_trim.25bp_2.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2.flexbar_trim.25bp_1.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2.flexbar_trim.25bp_2.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2.flexbar_trim.25bp_1.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2.flexbar_trim.25bp_2.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2.flexbar_trim.25bp_1.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2.flexbar_trim.25bp_2.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2.flexbar_trim.25bp_1.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2.flexbar_trim.25bp_2.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2.flexbar_trim.25bp_1.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-POC-57-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_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p_depths.txt samtools view -F 256 -f 16 -e "qlen==21" -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m_depths.txt samtools view -F 272 -e "qlen==22" -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p_depths.txt samtools view -F 256 -f 16 -e "qlen==22" -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m_depths.txt samtools view -F 272 -e "qlen==23 || qlen==24" -h /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-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_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-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_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-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_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m_depths.txt Writing wiggle files /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.wig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.bw wigToBigWig /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.wig chromSizes.txt /home/shared/8TB_HDD_02/shedurkin/deep-dive/F-Pmea/output/13-Pmea-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.bw Converting to sorted bam format Uniquely mapped (U) reads: 2665025/16574698 (16.1%) Multi-mapped reads placed (P) with guidance: 6625937/16574698 (40.0%) Multi-mapped reads randomly (R) placed: 4170549/16574698 (25.2%) Very highly (H) multi-mapped reads (>=50 hits): 175665/16574698 (1.1%) Not mapped (N) reads (no hits): 2937522/16574698 (17.7%) Thu 30 Nov 2023 16:52:38 -0800 PST Merging and indexing alignments Creating browser tracks by readgroup using ShortTracks Creating browser tracks by readlength and strand using ShortTracks Thu 30 Nov 2023 17:26:57 -0800 PST Defining small RNA clusters de novo With 163107256 total reads and mincov of 1 reads per million, the min read depth is 163 Thu 30 Nov 2023 17:27:17 -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... Thu 30 Nov 2023 17:30:26 -0800 PST Completed Thu 30 Nov 2023 17:30:26 -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 No microRNA loci were found! Writing final files Non-MIRNA loci by DicerCall: N 7191 23 45 22 39 21 18 24 13 Thu 30 Nov 2023 17:31:28 -0800 PST Run Completed! real 101m1.563s user 1946m43.958s sys 621m8.203s