# reads processed: 12066776
# reads with at least one alignment: 7535065 (62.44%)
# reads that failed to align: 4531711 (37.56%)
Reported 37442927 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-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out',
    'pad': 200,
    'readfile': [   '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-47-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-48-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-50-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-53-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.gz',
                    '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-57-S1-TP2-fastp-adapters-polyG-31bp-merged.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

Thu 06 Jun 2024 08:15:56 -0700 PDT
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-47-S1-TP2-fastp-adapters-polyG-31bp-merged.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: 14045042
# reads with at least one alignment: 8762911 (62.39%)
# reads that failed to align: 5282131 (37.61%)
Reported 39033925 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 2142481/12066776 (17.8%)
Multi-mapped reads placed (P) with guidance: 3401914/12066776 (28.2%)
Multi-mapped reads randomly (R) placed: 1913920/12066776 (15.9%)
Very highly (H) multi-mapped reads (>=50 hits): 76750/12066776 (0.6%)
Not mapped (N) reads (no hits): 4531711/12066776 (37.6%)

Thu 06 Jun 2024 08:20:20 -0700 PDT
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-48-S1-TP2-fastp-adapters-polyG-31bp-merged.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: 12141955
# reads with at least one alignment: 6786360 (55.89%)
# reads that failed to align: 5355595 (44.11%)
Reported 33750734 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 1810393/14045042 (12.9%)
Multi-mapped reads placed (P) with guidance: 4624242/14045042 (32.9%)
Multi-mapped reads randomly (R) placed: 2250675/14045042 (16.0%)
Very highly (H) multi-mapped reads (>=50 hits): 77601/14045042 (0.6%)
Not mapped (N) reads (no hits): 5282131/14045042 (37.6%)

Thu 06 Jun 2024 08:25:17 -0700 PDT
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-50-S1-TP2-fastp-adapters-polyG-31bp-merged.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: 15732665
# reads with at least one alignment: 11926432 (75.81%)
# reads that failed to align: 3806233 (24.19%)
Reported 45230690 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 1968136/12141955 (16.2%)
Multi-mapped reads placed (P) with guidance: 3222798/12141955 (26.5%)
Multi-mapped reads randomly (R) placed: 1507938/12141955 (12.4%)
Very highly (H) multi-mapped reads (>=50 hits): 87488/12141955 (0.7%)
Not mapped (N) reads (no hits): 5355595/12141955 (44.1%)

Thu 06 Jun 2024 08:29:43 -0700 PDT
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-53-S1-TP2-fastp-adapters-polyG-31bp-merged.fq.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: 14136486
# reads with at least one alignment: 11765022 (83.22%)
# reads that failed to align: 2371464 (16.78%)
Reported 40766404 alignments

Converting to sorted bam format
Uniquely mapped (U) reads: 2885541/15732665 (18.3%)
Multi-mapped reads placed (P) with guidance: 4775412/15732665 (30.4%)
Multi-mapped reads randomly (R) placed: 4167280/15732665 (26.5%)
Very highly (H) multi-mapped reads (>=50 hits): 98199/15732665 (0.6%)
Not mapped (N) reads (no hits): 3806233/15732665 (24.2%)

Thu 06 Jun 2024 08:35:18 -0700 PDT
Aligning /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/08.2-Pmea-sRNAseq-trimming-31bp-fastp-merged/trimmed-reads/sRNA-POC-57-S1-TP2-fastp-adapters-polyG-31bp-merged.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...
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-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt

samtools view -F 256 -r sRNA-POC-48-S1-TP2-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt

samtools view -F 256 -r sRNA-POC-50-S1-TP2-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt

samtools view -F 256 -r sRNA-POC-53-S1-TP2-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt

samtools view -F 256 -r sRNA-POC-57-S1-TP2-fastp-adapters-polyG-31bp-merged -h /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2-fastp-adapters-polyG-31bp-merged_depths.txt


Writing wiggle files
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2-fastp-adapters-polyG-31bp-merged.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2-fastp-adapters-polyG-31bp-merged.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2-fastp-adapters-polyG-31bp-merged.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2-fastp-adapters-polyG-31bp-merged.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2-fastp-adapters-polyG-31bp-merged.wig

Writing bigwig files
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-47-S1-TP2-fastp-adapters-polyG-31bp-merged.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-48-S1-TP2-fastp-adapters-polyG-31bp-merged.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-50-S1-TP2-fastp-adapters-polyG-31bp-merged.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-53-S1-TP2-fastp-adapters-polyG-31bp-merged.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-57-S1-TP2-fastp-adapters-polyG-31bp-merged.wig chromSizes.txt /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_sRNA-POC-57-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments.bam | samtools depth - > /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_23-24_m.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_p.wig
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_21_m.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_22_m.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_p.bw
wigToBigWig /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/F-Pmea/output/13.2.1-Pmea-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/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/merged_alignments_other_m.bw

Converting to sorted bam format
Uniquely mapped (U) reads: 2380882/14136486 (16.8%)
Multi-mapped reads placed (P) with guidance: 5594429/14136486 (39.6%)
Multi-mapped reads randomly (R) placed: 3688290/14136486 (26.1%)
Very highly (H) multi-mapped reads (>=50 hits): 101421/14136486 (0.7%)
Not mapped (N) reads (no hits): 2371464/14136486 (16.8%)

Thu 06 Jun 2024 08:40:10 -0700 PDT
Merging and indexing alignments

Creating browser tracks by readgroup using ShortTracks

Creating browser tracks by readlength and strand using ShortTracks

Thu 06 Jun 2024 08:52:50 -0700 PDT
Defining small RNA clusters de novo
With 68122924 total reads and mincov of 1 reads per million, the min read depth is 68

Thu 06 Jun 2024 08:53:10 -0700 PDT
Analyzing cluster properties using 46 threads
# reads processed: 49415
# reads with at least one alignment: 171 (0.35%)
# reads that failed to align: 49244 (99.65%)
Reported 1856 alignments
[bam_sort_core] merging from 0 files and 46 in-memory blocks...

Thu 06 Jun 2024 08:54:48 -0700 PDT
 Completed

Thu 06 Jun 2024 08:54:48 -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

Thu 06 Jun 2024 08:55:21 -0700 PDT
Analyzing cluster properties using 46 threads

Thu 06 Jun 2024 08:55:25 -0700 PDT
 Completed

Writing final files

Found a total of 37 MIRNA loci


Non-MIRNA loci by DicerCall:
N 7087
22 33
23 33
24 15
21 15

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

Thu 06 Jun 2024 08:55:50 -0700 PDT
Run Completed!

real	39m54.805s
user	726m24.259s
sys	252m56.657s