# reads processed: 12209385
# reads with at least one alignment: 7770144 (63.64%)
# reads that failed to align: 4439241 (36.36%)
Reported 39568567 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/F-Pmea/data/Pocillopora_meandrina_HIv1.assembly.fa',
    'known_miRNAs': '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/cnidarian_miRNAs.fasta',
    'locifile': None,
    'locus': None,
    'mincov': 1,
    'mmap': 'u',
    'nohp': False,
    'outdir': '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out',
    'pad': 200,
    'readfile': [   '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz'],
    'show_secondaries': False,
    'strand_cutoff': 0.8,
    'threads': 46}
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

Fri 16 Feb 2024 12:50:40 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz
First pass alignment with bowtie using 46 threads
Second pass - placing multimappers using 46 threads to process 13 chunks
[bam_sort_core] merging from 0 files and 46 in-memory blocks...
# reads processed: 14848953
# reads with at least one alignment: 9561271 (64.39%)
# reads that failed to align: 5287682 (35.61%)
Reported 43777557 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 2133823/12209385 (17.5%)
Multi-mapped reads placed (P) with guidance: 3593492/12209385 (29.4%)
Multi-mapped reads randomly (R) placed: 1945356/12209385 (15.9%)
Very highly (H) multi-mapped reads (>=50 hits): 97473/12209385 (0.8%)
Not mapped (N) reads (no hits): 4439241/12209385 (36.4%)

Fri 16 Feb 2024 12:56:17 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.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: 12625701
# reads with at least one alignment: 7270826 (57.59%)
# reads that failed to align: 5354875 (42.41%)
Reported 37364807 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 1899373/14848953 (12.8%)
Multi-mapped reads placed (P) with guidance: 5232545/14848953 (35.2%)
Multi-mapped reads randomly (R) placed: 2322738/14848953 (15.6%)
Very highly (H) multi-mapped reads (>=50 hits): 106615/14848953 (0.7%)
Not mapped (N) reads (no hits): 5287682/14848953 (35.6%)

Fri 16 Feb 2024 13:02:27 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.gz
First pass alignment with bowtie using 46 threads
Second pass - placing multimappers using 46 threads to process 13 chunks
[bam_sort_core] merging from 0 files and 46 in-memory blocks...
# reads processed: 16831731
# reads with at least one alignment: 12867279 (76.45%)
# reads that failed to align: 3964452 (23.55%)
Reported 51533602 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 2021257/12625701 (16.0%)
Multi-mapped reads placed (P) with guidance: 3576274/12625701 (28.3%)
Multi-mapped reads randomly (R) placed: 1559388/12625701 (12.4%)
Very highly (H) multi-mapped reads (>=50 hits): 113907/12625701 (0.9%)
Not mapped (N) reads (no hits): 5354875/12625701 (42.4%)

Fri 16 Feb 2024 13:07:56 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.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: 16502248
# reads with at least one alignment: 14062854 (85.22%)
# reads that failed to align: 2439394 (14.78%)
Reported 53449399 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 2930776/16831731 (17.4%)
Multi-mapped reads placed (P) with guidance: 5525433/16831731 (32.8%)
Multi-mapped reads randomly (R) placed: 4279720/16831731 (25.4%)
Very highly (H) multi-mapped reads (>=50 hits): 131350/16831731 (0.8%)
Not mapped (N) reads (no hits): 3964452/16831731 (23.6%)

Fri 16 Feb 2024 13:15:06 -0800 PST
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.1-Pmea-sRNAseq-trimming-R1-only/trimmed-reads/sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.fq.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/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-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt

samtools view -F 256 -r sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt

samtools view -F 256 -r sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt

samtools view -F 256 -r sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt

samtools view -F 256 -r sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG_depths.txt


Writing wiggle files
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig

Writing bigwig files
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2_R1_001.fastp-R1-31bp-auto_adapters-polyG.bw
ShortTracks version 1.1

Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/samtools
Required executable wigToBigWig : /home/sam/programs/mambaforge/envs/ShortStack-4.0.3_env/bin/wigToBigWig

Preparing commands, counting overall reads

Getting raw depths
samtools view -F 272 -e "qlen==21" -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-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/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-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/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-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/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-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/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-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/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-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/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-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/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m_depths.txt


Writing wiggle files
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_21_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_21_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_22_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_22_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_other_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m.wig

Writing bigwig files
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_21_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_21_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_21_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_21_m.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_22_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_22_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_22_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_22_m.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_m.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_other_p.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_other_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.1.1-Pmea-sRNAseq-ShortStack-R1-reads-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m.bw

Converting to sorted bam format
Uniquely mapped (U) reads: 2627232/16502248 (15.9%)
Multi-mapped reads placed (P) with guidance: 7239113/16502248 (43.9%)
Multi-mapped reads randomly (R) placed: 4025353/16502248 (24.4%)
Very highly (H) multi-mapped reads (>=50 hits): 171156/16502248 (1.0%)
Not mapped (N) reads (no hits): 2439394/16502248 (14.8%)

Fri 16 Feb 2024 13:22:12 -0800 PST
Merging and indexing alignments

Creating browser tracks by readgroup using ShortTracks

Creating browser tracks by readlength and strand using ShortTracks

Fri 16 Feb 2024 13:36:37 -0800 PST
Defining small RNA clusters de novo
With 73018018 total reads and mincov of 1 reads per million, the min read depth is 73

Fri 16 Feb 2024 13:36:58 -0800 PST
Analyzing cluster properties using 46 threads
# reads processed: 530
# reads with at least one alignment: 60 (11.32%)
# reads that failed to align: 470 (88.68%)
Reported 142 alignments

Fri 16 Feb 2024 13:38:54 -0800 PST
 Completed

Fri 16 Feb 2024 13:38:54 -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

Fri 16 Feb 2024 13:39:26 -0800 PST
Analyzing cluster properties using 46 threads

Fri 16 Feb 2024 13:39:31 -0800 PST
 Completed

Writing final files

Found a total of 36 MIRNA loci


Non-MIRNA loci by DicerCall:
N 7713
23 37
22 31
24 14
21 9

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

Fri 16 Feb 2024 13:39:56 -0800 PST
Run Completed!

real	49m15.895s
user	919m37.072s
sys	320m22.844s