# reads processed: 17551962
# reads with at least one alignment: 13153828 (74.94%)
# reads that failed to align: 4398134 (25.06%)
Reported 88647131 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/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-Apul-sRNAseq-ShortStack/ShortStack_out',
    'pad': 200,
    'readfile': [   '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_1.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_2.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_1.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_2.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_1.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_2.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_1.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_2.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_1.fastq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-178-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

Mon 06 Nov 2023 09:28:00 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-140-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: 17551962
# reads with at least one alignment: 12617446 (71.89%)
# reads that failed to align: 4934516 (28.11%)
Reported 82451872 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 3933784/17551962 (22.4%)
Multi-mapped reads placed (P) with guidance: 6931966/17551962 (39.5%)
Multi-mapped reads randomly (R) placed: 1920447/17551962 (10.9%)
Very highly (H) multi-mapped reads (>=50 hits): 367631/17551962 (2.1%)
Not mapped (N) reads (no hits): 4398134/17551962 (25.1%)

Mon 06 Nov 2023 09:37:20 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-140-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...
# reads processed: 19892972
# reads with at least one alignment: 14847194 (74.64%)
# reads that failed to align: 5045778 (25.36%)
Reported 111688583 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 4073677/17551962 (23.2%)
Multi-mapped reads placed (P) with guidance: 6715702/17551962 (38.3%)
Multi-mapped reads randomly (R) placed: 1504410/17551962 (8.6%)
Very highly (H) multi-mapped reads (>=50 hits): 323657/17551962 (1.8%)
Not mapped (N) reads (no hits): 4934516/17551962 (28.1%)

Mon 06 Nov 2023 09:45:20 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-145-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 20 chunks
[bam_sort_core] merging from 0 files and 46 in-memory blocks...
# reads processed: 19892972
# reads with at least one alignment: 14292162 (71.85%)
# reads that failed to align: 5600810 (28.15%)
Reported 104482342 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 4147846/19892972 (20.9%)
Multi-mapped reads placed (P) with guidance: 8254255/19892972 (41.5%)
Multi-mapped reads randomly (R) placed: 1947764/19892972 (9.8%)
Very highly (H) multi-mapped reads (>=50 hits): 497329/19892972 (2.5%)
Not mapped (N) reads (no hits): 5045778/19892972 (25.4%)

Mon 06 Nov 2023 09:56:33 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-145-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 20 chunks
[bam_sort_core] merging from 0 files and 46 in-memory blocks...
# reads processed: 21281386
# reads with at least one alignment: 15008659 (70.52%)
# reads that failed to align: 6272727 (29.48%)
Reported 98717419 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 4276923/19892972 (21.5%)
Multi-mapped reads placed (P) with guidance: 8005930/19892972 (40.2%)
Multi-mapped reads randomly (R) placed: 1562359/19892972 (7.9%)
Very highly (H) multi-mapped reads (>=50 hits): 446950/19892972 (2.2%)
Not mapped (N) reads (no hits): 5600810/19892972 (28.2%)

Mon 06 Nov 2023 10:07:41 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-150-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 22 chunks
[bam_sort_core] merging from 0 files and 46 in-memory blocks...
# reads processed: 21281386
# reads with at least one alignment: 14456522 (67.93%)
# reads that failed to align: 6824864 (32.07%)
Reported 91133795 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 4813678/21281386 (22.6%)
Multi-mapped reads placed (P) with guidance: 7925230/21281386 (37.2%)
Multi-mapped reads randomly (R) placed: 1831668/21281386 (8.6%)
Very highly (H) multi-mapped reads (>=50 hits): 438083/21281386 (2.1%)
Not mapped (N) reads (no hits): 6272727/21281386 (29.5%)

Mon 06 Nov 2023 10:18:45 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-150-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 22 chunks
[bam_sort_core] merging from 0 files and 46 in-memory blocks...
# reads processed: 18566189
# reads with at least one alignment: 13728064 (73.94%)
# reads that failed to align: 4838125 (26.06%)
Reported 96168469 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 5428895/21281386 (25.5%)
Multi-mapped reads placed (P) with guidance: 7112683/21281386 (33.4%)
Multi-mapped reads randomly (R) placed: 1519953/21281386 (7.1%)
Very highly (H) multi-mapped reads (>=50 hits): 394991/21281386 (1.9%)
Not mapped (N) reads (no hits): 6824864/21281386 (32.1%)

Mon 06 Nov 2023 10:29:11 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-173-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: 18566189
# reads with at least one alignment: 13144453 (70.80%)
# reads that failed to align: 5421736 (29.20%)
Reported 89922997 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 3981521/18566189 (21.4%)
Multi-mapped reads placed (P) with guidance: 7480935/18566189 (40.3%)
Multi-mapped reads randomly (R) placed: 1879761/18566189 (10.1%)
Very highly (H) multi-mapped reads (>=50 hits): 385847/18566189 (2.1%)
Not mapped (N) reads (no hits): 4838125/18566189 (26.1%)

Mon 06 Nov 2023 10:39:49 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-173-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: 16505612
# reads with at least one alignment: 11888694 (72.03%)
# reads that failed to align: 4616918 (27.97%)
Reported 89315791 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 4069184/18566189 (21.9%)
Multi-mapped reads placed (P) with guidance: 7265600/18566189 (39.1%)
Multi-mapped reads randomly (R) placed: 1468050/18566189 (7.9%)
Very highly (H) multi-mapped reads (>=50 hits): 341619/18566189 (1.8%)
Not mapped (N) reads (no hits): 5421736/18566189 (29.2%)

Mon 06 Nov 2023 10:49:52 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-178-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: 16505612
# reads with at least one alignment: 11708620 (70.94%)
# reads that failed to align: 4796992 (29.06%)
Reported 84271258 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 3448866/16505612 (20.9%)
Multi-mapped reads placed (P) with guidance: 6471973/16505612 (39.2%)
Multi-mapped reads randomly (R) placed: 1521737/16505612 (9.2%)
Very highly (H) multi-mapped reads (>=50 hits): 446118/16505612 (2.7%)
Not mapped (N) reads (no hits): 4616918/16505612 (28.0%)

Mon 06 Nov 2023 10:59:35 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/08-Apul-sRNAseq-trimming/trimmed-reads/sRNA-ACR-178-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-ACR-140-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_1_depths.txt

samtools view -F 256 -r sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_2_depths.txt

samtools view -F 256 -r sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_1_depths.txt

samtools view -F 256 -r sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_2_depths.txt

samtools view -F 256 -r sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_1_depths.txt

samtools view -F 256 -r sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_2_depths.txt

samtools view -F 256 -r sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_1_depths.txt

samtools view -F 256 -r sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_2_depths.txt

samtools view -F 256 -r sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_1 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_1_depths.txt

samtools view -F 256 -r sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_2 -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_2_depths.txt


Writing wiggle files
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_1.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_2.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_1.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_2.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_1.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_2.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_1.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_2.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_1.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_2.wig

Writing bigwig files
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_1.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-140-S1-TP2.flexbar_trim.25bp_2.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_1.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-145-S1-TP2.flexbar_trim.25bp_2.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_1.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-150-S1-TP2.flexbar_trim.25bp_2.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_1.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-173-S1-TP2.flexbar_trim.25bp_2.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_1.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_1.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-178-S1-TP2.flexbar_trim.25bp_2.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_sRNA-ACR-178-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/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-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/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-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/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-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/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-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/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-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/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-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/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-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/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m_depths.txt


Writing wiggle files
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.wig

Writing bigwig files
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_21_m.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_22_m.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_23-24_m.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack_out/merged_alignments_other_m.bw

Converting to sorted bam format
Uniquely mapped (U) reads: 3563536/16505612 (21.6%)
Multi-mapped reads placed (P) with guidance: 6486176/16505612 (39.3%)
Multi-mapped reads randomly (R) placed: 1305382/16505612 (7.9%)
Very highly (H) multi-mapped reads (>=50 hits): 353526/16505612 (2.1%)
Not mapped (N) reads (no hits): 4796992/16505612 (29.1%)

Mon 06 Nov 2023 11:08:16 -0800 PST
Merging and indexing alignments

Creating browser tracks by readgroup using ShortTracks

Creating browser tracks by readlength and strand using ShortTracks

Mon 06 Nov 2023 11:48:28 -0800 PST
Defining small RNA clusters de novo
With 187596242 total reads and mincov of 1 reads per million, the min read depth is 188

Mon 06 Nov 2023 11:48:53 -0800 PST
Analyzing cluster properties using 46 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 46 in-memory blocks...

Mon 06 Nov 2023 11:50:29 -0800 PST
 Completed

Mon 06 Nov 2023 11:50:29 -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 18676
22 45
23 36
21 10
24 5

Mon 06 Nov 2023 11:50:36 -0800 PST
Run Completed!

real	142m36.973s
user	2955m32.601s
sys	1100m59.754s