# reads processed: 15076001 # reads with at least one alignment: 10592185 (70.26%) # reads that failed to align: 4483816 (29.74%) Reported 64484455 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/cnidarian-mirbase-mature-v22.1.fasta', 'locifile': None, 'locus': None, 'mincov': 1, 'mmap': 'u', 'nohp': False, 'outdir': '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out', 'pad': 200, 'readfile': [ '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-145-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-150-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-173-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.gz', '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-178-S1-TP2-fastp-adapters-polyG-31bp-merged.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 Tue 02 Apr 2024 08:10:22 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.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: 17265123 # reads with at least one alignment: 12360919 (71.59%) # reads that failed to align: 4904204 (28.41%) Reported 83736172 alignments Converting to sorted bam format Uniquely mapped (U) reads: 3645522/15076001 (24.2%) Multi-mapped reads placed (P) with guidance: 5244401/15076001 (34.8%) Multi-mapped reads randomly (R) placed: 1455985/15076001 (9.7%) Very highly (H) multi-mapped reads (>=50 hits): 246277/15076001 (1.6%) Not mapped (N) reads (no hits): 4483816/15076001 (29.7%) Tue 02 Apr 2024 08:15:40 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-145-S1-TP2-fastp-adapters-polyG-31bp-merged.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: 18395038 # reads with at least one alignment: 12479638 (67.84%) # reads that failed to align: 5915400 (32.16%) Reported 74060078 alignments Converting to sorted bam format Uniquely mapped (U) reads: 3952155/17265123 (22.9%) Multi-mapped reads placed (P) with guidance: 6528712/17265123 (37.8%) Multi-mapped reads randomly (R) placed: 1521245/17265123 (8.8%) Very highly (H) multi-mapped reads (>=50 hits): 358807/17265123 (2.1%) Not mapped (N) reads (no hits): 4904204/17265123 (28.4%) Tue 02 Apr 2024 08:22:05 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-150-S1-TP2-fastp-adapters-polyG-31bp-merged.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: 16332044 # reads with at least one alignment: 11437223 (70.03%) # reads that failed to align: 4894821 (29.97%) Reported 72428783 alignments Converting to sorted bam format Uniquely mapped (U) reads: 4809502/18395038 (26.1%) Multi-mapped reads placed (P) with guidance: 5892102/18395038 (32.0%) Multi-mapped reads randomly (R) placed: 1463152/18395038 (8.0%) Very highly (H) multi-mapped reads (>=50 hits): 314882/18395038 (1.7%) Not mapped (N) reads (no hits): 5915400/18395038 (32.2%) Tue 02 Apr 2024 08:27:57 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-173-S1-TP2-fastp-adapters-polyG-31bp-merged.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: 14295261 # reads with at least one alignment: 10030101 (70.16%) # reads that failed to align: 4265160 (29.84%) Reported 68014076 alignments Converting to sorted bam format Uniquely mapped (U) reads: 3753892/16332044 (23.0%) Multi-mapped reads placed (P) with guidance: 5995171/16332044 (36.7%) Multi-mapped reads randomly (R) placed: 1425253/16332044 (8.7%) Very highly (H) multi-mapped reads (>=50 hits): 262907/16332044 (1.6%) Not mapped (N) reads (no hits): 4894821/16332044 (30.0%) Tue 02 Apr 2024 08:33:37 -0700 PDT Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08.2-Apul-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-ACR-178-S1-TP2-fastp-adapters-polyG-31bp-merged.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-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt samtools view -F 256 -r sRNA-ACR-145-S1-TP2-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt samtools view -F 256 -r sRNA-ACR-150-S1-TP2-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt samtools view -F 256 -r sRNA-ACR-173-S1-TP2-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt samtools view -F 256 -r sRNA-ACR-178-S1-TP2-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt Writing wiggle files /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2-fastp-adapters-polyG-31bp-merged.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2-fastp-adapters-polyG-31bp-merged.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2-fastp-adapters-polyG-31bp-merged.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2-fastp-adapters-polyG-31bp-merged.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2-fastp-adapters-polyG-31bp-merged.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2-fastp-adapters-polyG-31bp-merged.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2-fastp-adapters-polyG-31bp-merged.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2-fastp-adapters-polyG-31bp-merged.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/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/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/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/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/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/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/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/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/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/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/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/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/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/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/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m_depths.txt Writing wiggle files /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_m.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_p.wig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m.wig Writing bigwig files wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_m.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_p.bw wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m.bw Converting to sorted bam format Uniquely mapped (U) reads: 3250739/14295261 (22.7%) Multi-mapped reads placed (P) with guidance: 5275125/14295261 (36.9%) Multi-mapped reads randomly (R) placed: 1210521/14295261 (8.5%) Very highly (H) multi-mapped reads (>=50 hits): 293716/14295261 (2.1%) Not mapped (N) reads (no hits): 4265160/14295261 (29.8%) Tue 02 Apr 2024 08:38:53 -0700 PDT Merging and indexing alignments Creating browser tracks by readgroup using ShortTracks Creating browser tracks by readlength and strand using ShortTracks Tue 02 Apr 2024 08:54:35 -0700 PDT Defining small RNA clusters de novo With 81363467 total reads and mincov of 1 reads per million, the min read depth is 81 Tue 02 Apr 2024 08:54:58 -0700 PDT Analyzing cluster properties using 40 threads # reads processed: 49415 # reads with at least one alignment: 148 (0.30%) # reads that failed to align: 49267 (99.70%) Reported 1446 alignments [bam_sort_core] merging from 0 files and 40 in-memory blocks... Tue 02 Apr 2024 08:55:50 -0700 PDT Completed Tue 02 Apr 2024 08:55:50 -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 Tue 02 Apr 2024 08:56:01 -0700 PDT Analyzing cluster properties using 40 threads Warning: the index file is older than the FASTA file. Tue 02 Apr 2024 08:56:07 -0700 PDT Completed Writing final files Found a total of 38 MIRNA loci Non-MIRNA loci by DicerCall: N 18768 22 39 23 32 21 12 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 Tue 02 Apr 2024 08:56:32 -0700 PDT Run Completed! real 46m10.802s user 779m56.322s sys 253m43.749s