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gatk-pipeline-commands.html
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<div id='write' class = 'is-node'><h1><a name='header-n250' class='md-header-anchor '></a>gatk pipeline with snakemake</h1><p>Output of the following command have been annotated</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">snakemake <span class="cm-attribute">-p</span> <span class="cm-attribute">--use-conda</span> <span class="cm-attribute">--cores</span> <span class="cm-number">8</span> > gatk-pipeline-commands <span class="cm-number">2</span>>&1</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 20px;"></div><div class="CodeMirror-gutters" style="display: none; height: 20px;"></div></div></div></pre><h2><a name='header-n254' class='md-header-anchor '></a>Info</h2><p>/home/alper/miniconda3/lib/python3.7/site-packages/snakemake/workflow.py:12: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
from collections import OrderedDict
/home/alper/miniconda3/lib/python3.7/site-packages/snakemake/workflow.py:15: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
from operator import attrgetter
/home/alper/miniconda3/lib/python3.7/site-packages/snakemake/workflow.py:21: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
from snakemake.exceptions import RuleException, CreateRuleException, \
Building DAG of jobs...
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Using shell: /bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job counts:
<span> </span>count<span> </span>jobs
<span> </span>1<span> </span>all
<span> </span>2<span> </span>call_variants
<span> </span>1<span> </span>combine_calls
<span> </span>3<span> </span>fastqc
<span> </span>1<span> </span>genotype_variants
<span> </span>2<span> </span>hard_filter_calls
<span> </span>3<span> </span>map_reads
<span> </span>3<span> </span>mark_duplicates
<span> </span>1<span> </span>merge_calls
<span> </span>1<span> </span>merge_variants
<span> </span>1<span> </span>multiqc
<span> </span>1<span> </span>plot_stats
<span> </span>3<span> </span>recalibrate_base_qualities
<span> </span>3<span> </span>samtools_stats
<span> </span>2<span> </span>select_calls
<span> </span>1<span> </span>snpeff
<span> </span>2<span> </span>trim_reads_pe
<span> </span>1<span> </span>trim_reads_se
<span> </span>1<span> </span>vcf_to_tsv
<span> </span>33</p><h2><a name='header-n256' class='md-header-anchor '></a>job1 : trim_reads_se</h2><p> </p><p>[Mon Apr 29 10:37:26 2019]
rule trim_reads_se:
input: data/reads/b.chr21.1.fq
output: trimmed/B-2.fastq.gz
log: logs/trimmomatic/B-2.log
jobid: 27
wildcards: sample=B, unit=2</p><p>[Mon Apr 29 10:37:26 2019]
rule trim_reads_pe:
input: data/reads/b.chr21.1.fq, data/reads/b.chr21.2.fq
output: trimmed/B-1.1.fastq.gz, trimmed/B-1.2.fastq.gz, trimmed/B-1.1.unpaired.fastq.gz, trimmed/B-1.2.unpaired.fastq.gz, trimmed/B-1.trimlog.txt
log: logs/trimmomatic/B-1.log
jobid: 26
wildcards: sample=B, unit=1</p><p>[Mon Apr 29 10:37:26 2019]
rule trim_reads_pe:
input: data/reads/a.chr21.1.fq, data/reads/a.chr21.2.fq
output: trimmed/A-1.1.fastq.gz, trimmed/A-1.2.fastq.gz, trimmed/A-1.1.unpaired.fastq.gz, trimmed/A-1.2.unpaired.fastq.gz, trimmed/A-1.trimlog.txt
log: logs/trimmomatic/A-1.log
jobid: 25
wildcards: sample=A, unit=1</p><p>[Mon Apr 29 10:37:26 2019]
rule fastqc:
input: data/reads/b.chr21.1.fq
output: qc/fastqc/B-2.html, qc/fastqc/B-2.zip
jobid: 12
wildcards: sample=B, unit=2</p><p>[Mon Apr 29 10:37:26 2019]
rule fastqc:
input: data/reads/b.chr21.1.fq, data/reads/b.chr21.2.fq
output: qc/fastqc/B-1.html, qc/fastqc/B-1.zip
jobid: 9
wildcards: sample=B, unit=1</p><p>[Mon Apr 29 10:37:26 2019]
rule fastqc:
input: data/reads/a.chr21.1.fq, data/reads/a.chr21.2.fq
output: qc/fastqc/A-1.html, qc/fastqc/A-1.zip
jobid: 6
wildcards: sample=A, unit=1</p><p>/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpdu7k4w0<em>.wrapper.py
/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmp3m4byz_e.wrapper.py
/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpu9u4sqgl.wrapper.py
/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpqczx5dpr.wrapper.py
/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmp8nr4i52y.wrapper.py
/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpt1scdsu</em>.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/c0b8860d
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/c0b8860d
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/c0b8860d
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/e0139b03
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/e0139b03
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/e0139b03</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">trimmomatic PE -trimlog trimmed/A-1.trimlog.txt data/reads/a.chr21.1.fq data/reads/a.chr21.2.fq >(pigz -5 > trimmed/A-1.1.fastq.gz) >(pigz -5 > trimmed/A-1.1.unpaired.fastq.gz) >(pigz -5 > trimmed/A-1.2.fastq.gz) >(pigz -5 > trimmed/A-1.2.unpaired.fastq.gz) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 > logs/trimmomatic/A-1.log 2>&1</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">trimmomatic SE data/reads/b.chr21.1.fq >(pigz -5 > trimmed/B-2.fastq.gz) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 > logs/trimmomatic/B-2.log 2>&1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">fastqc --quiet --outdir /tmp/tmp8a3c359i data/reads/b.chr21.1.fq </span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">trimmomatic PE -trimlog trimmed/B-1.trimlog.txt data/reads/b.chr21.1.fq data/reads/b.chr21.2.fq >(pigz -5 > trimmed/B-1.1.fastq.gz) >(pigz -5 > trimmed/B-1.1.unpaired.fastq.gz) >(pigz -5 > trimmed/B-1.2.fastq.gz) >(pigz -5 > trimmed/B-1.2.unpaired.fastq.gz) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 > logs/trimmomatic/B-1.log 2>&1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">fastqc --quiet --outdir /tmp/tmp902azgfu data/reads/b.chr21.1.fq </span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">fastqc --quiet --outdir /tmp/tmpaqjqld16 data/reads/a.chr21.1.fq </span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 320px;"></div><div class="CodeMirror-gutters" style="display: none; height: 320px;"></div></div></div></pre><p>[Mon Apr 29 10:37:29 2019]
Finished job 27.
1 of 33 steps (3%) done
Removing temporary output file trimmed/A-1.1.unpaired.fastq.gz.
Removing temporary output file trimmed/A-1.2.unpaired.fastq.gz.
[Mon Apr 29 10:37:31 2019]
Finished job 25.
2 of 33 steps (6%) done
Removing temporary output file trimmed/B-1.1.unpaired.fastq.gz.
Removing temporary output file trimmed/B-1.2.unpaired.fastq.gz.
[Mon Apr 29 10:37:31 2019]
Finished job 26.
3 of 33 steps (9%) done
mv /tmp/tmp8a3c359i/b.chr21.1_fastqc.html qc/fastqc/B-1.html
mv /tmp/tmp8a3c359i/b.chr21.1_fastqc.zip qc/fastqc/B-1.zip
[Mon Apr 29 10:37:33 2019]
Finished job 9.
4 of 33 steps (12%) done
mv /tmp/tmp902azgfu/b.chr21.1_fastqc.html qc/fastqc/B-2.html
mv /tmp/tmp902azgfu/b.chr21.1_fastqc.zip qc/fastqc/B-2.zip
[Mon Apr 29 10:37:33 2019]
Finished job 12.
5 of 33 steps (15%) done
mv /tmp/tmpaqjqld16/a.chr21.1_fastqc.html qc/fastqc/A-1.html
mv /tmp/tmpaqjqld16/a.chr21.1_fastqc.zip qc/fastqc/A-1.zip
[Mon Apr 29 10:37:33 2019]
Finished job 6.
6 of 33 steps (18%) done</p><p>[Mon Apr 29 10:37:29 2019]
Finished job 27.
1 of 33 steps (3%) done
Removing temporary output file trimmed/A-1.1.unpaired.fastq.gz.
Removing temporary output file trimmed/A-1.2.unpaired.fastq.gz.
[Mon Apr 29 10:37:31 2019]
Finished job 25.
2 of 33 steps (6%) done
Removing temporary output file trimmed/B-1.1.unpaired.fastq.gz.
Removing temporary output file trimmed/B-1.2.unpaired.fastq.gz.
[Mon Apr 29 10:37:31 2019]
Finished job 26.
3 of 33 steps (9%) done
mv /tmp/tmp8a3c359i/b.chr21.1_fastqc.html qc/fastqc/B-1.html
mv /tmp/tmp8a3c359i/b.chr21.1_fastqc.zip qc/fastqc/B-1.zip
[Mon Apr 29 10:37:33 2019]
Finished job 9.
4 of 33 steps (12%) done
mv /tmp/tmp902azgfu/b.chr21.1_fastqc.html qc/fastqc/B-2.html
mv /tmp/tmp902azgfu/b.chr21.1_fastqc.zip qc/fastqc/B-2.zip
[Mon Apr 29 10:37:33 2019]
Finished job 12.
5 of 33 steps (15%) done
mv /tmp/tmpaqjqld16/a.chr21.1_fastqc.html qc/fastqc/A-1.html
mv /tmp/tmpaqjqld16/a.chr21.1_fastqc.zip qc/fastqc/A-1.zip
[Mon Apr 29 10:37:33 2019]
Finished job 6.
6 of 33 steps (18%) done</p><p>[Mon Apr 29 10:37:33 2019]
rule map_reads:
input: trimmed/B-1.1.fastq.gz, trimmed/B-1.2.fastq.gz
output: mapped/B-1.sorted.bam
log: logs/bwa_mem/B-1.log
jobid: 20
wildcards: sample=B, unit=1
threads: 8</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpmqx3dygi.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/332db904</p><p>Removing temporary output file trimmed/B-1.2.fastq.gz.
Removing temporary output file trimmed/B-1.1.fastq.gz.
[Mon Apr 29 10:37:36 2019]
Finished job 20.
7 of 33 steps (21%) done</p><p>[Mon Apr 29 10:37:36 2019]
rule mark_duplicates:
input: mapped/B-1.sorted.bam
output: dedup/B-1.bam, qc/dedup/B-1.metrics.txt
log: logs/picard/dedup/B-1.log
jobid: 10
wildcards: sample=B, unit=1</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmp0ap4algq.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/931cfa38</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">picard MarkDuplicates REMOVE_DUPLICATES=true INPUT=mapped/B-1.sorted.bam OUTPUT=dedup/B-1.bam METRICS_FILE=qc/dedup/B-1.metrics.txt &> logs/picard/dedup/B-1.log</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 40px;"></div><div class="CodeMirror-gutters" style="display: none; height: 40px;"></div></div></div></pre><p>Removing temporary output file mapped/B-1.sorted.bam.
[Mon Apr 29 10:37:39 2019]
Finished job 10.
8 of 33 steps (24%) done</p><p>Removing temporary output file mapped/B-1.sorted.bam.
[Mon Apr 29 10:37:39 2019]
Finished job 10.
8 of 33 steps (24%) done</p><p>[Mon Apr 29 10:37:39 2019]
rule recalibrate_base_qualities:
input: dedup/B-1.bam, data/ref/genome.chr21.fa, data/ref/dbsnp.vcf.gz
output: recal/B-1.bam
log: logs/gatk/bqsr/B-1.log
jobid: 19
wildcards: sample=B, unit=1</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmplo6c1ww2.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk BaseRecalibrator -R data/ref/genome.chr21.fa -I dedup/B-1.bam -O /tmp/tmpz_7des4i/recal_table.grp --known-sites data/ref/dbsnp.vcf.gz > logs/gatk/bqsr/B-1.log 2>&1</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk ApplyBQSR -R data/ref/genome.chr21.fa -I dedup/B-1.bam --bqsr-recal-file /tmp/tmpz_7des4i/recal_table.grp -O recal/B-1.bam >> logs/gatk/bqsr/B-1.log 2>&1</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 100px;"></div><div class="CodeMirror-gutters" style="display: none; height: 100px;"></div></div></div></pre><p>Write-protecting output file recal/B-1.bam.
Removing temporary output file dedup/B-1.bam.
[Mon Apr 29 10:37:47 2019]
Finished job 19.
9 of 33 steps (27%) done</p><p>[Mon Apr 29 10:37:47 2019]
rule map_reads:
input: trimmed/A-1.1.fastq.gz, trimmed/A-1.2.fastq.gz
output: mapped/A-1.sorted.bam
log: logs/bwa_mem/A-1.log
jobid: 18
wildcards: sample=A, unit=1
threads: 8</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpiklthufk.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/332db904</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">(bwa mem -t 8 -R '@RG\tID:A\tSM:A\tPL:ILLUMINA' data/ref/genome.chr21.fa trimmed/A-1.1.fastq.gz trimmed/A-1.2.fastq.gz | samtools sort -T mapped/A-1.sorted.tmp -o mapped/A-1.sorted.bam -) 2> logs/bwa_mem/A-1.log</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 60px;"></div><div class="CodeMirror-gutters" style="display: none; height: 60px;"></div></div></div></pre><p>Removing temporary output file trimmed/A-1.1.fastq.gz.
Removing temporary output file trimmed/A-1.2.fastq.gz.
[Mon Apr 29 10:37:50 2019]
Finished job 18.
10 of 33 steps (30%) done</p><p>[Mon Apr 29 10:37:50 2019]
rule mark_duplicates:
input: mapped/A-1.sorted.bam
output: dedup/A-1.bam, qc/dedup/A-1.metrics.txt
log: logs/picard/dedup/A-1.log
jobid: 7
wildcards: sample=A, unit=1</p><p>[Mon Apr 29 10:37:50 2019]
rule samtools_stats:
input: recal/B-1.bam
output: qc/samtools-stats/B-1.txt
log: logs/samtools-stats/B-1.log
jobid: 8
wildcards: sample=B, unit=1</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmp80_usdbx.wrapper.py
/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpyek85neo.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/931cfa38
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/c70824eb</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">picard MarkDuplicates REMOVE_DUPLICATES=true INPUT=mapped/A-1.sorted.bam OUTPUT=dedup/A-1.bam METRICS_FILE=qc/dedup/A-1.metrics.txt &> logs/picard/dedup/A-1.log</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">samtools stats recal/B-1.bam > qc/samtools-stats/B-1.txt 2> logs/samtools-stats/B-1.log</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 80px;"></div><div class="CodeMirror-gutters" style="display: none; height: 80px;"></div></div></div></pre><p>[Mon Apr 29 10:37:52 2019]
Finished job 8.
11 of 33 steps (33%) done
Removing temporary output file mapped/A-1.sorted.bam.
[Mon Apr 29 10:37:53 2019]
Finished job 7.
12 of 33 steps (36%) done</p><p>[Mon Apr 29 10:37:53 2019]
rule recalibrate_base_qualities:
input: dedup/A-1.bam, data/ref/genome.chr21.fa, data/ref/dbsnp.vcf.gz
output: recal/A-1.bam
log: logs/gatk/bqsr/A-1.log
jobid: 17
wildcards: sample=A, unit=1</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpbxlrkm83.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk BaseRecalibrator -R data/ref/genome.chr21.fa -I dedup/A-1.bam -O /tmp/tmprrlv1m03/recal_table.grp --known-sites data/ref/dbsnp.vcf.gz > logs/gatk/bqsr/A-1.log 2>&1</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk ApplyBQSR -R data/ref/genome.chr21.fa -I dedup/A-1.bam --bqsr-recal-file /tmp/tmprrlv1m03/recal_table.grp -O recal/A-1.bam >> logs/gatk/bqsr/A-1.log 2>&1</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 120px;"></div><div class="CodeMirror-gutters" style="display: none; height: 120px;"></div></div></div></pre><blockquote><p>Write-protecting output file recal/A-1.bam.
Removing temporary output file dedup/A-1.bam.</p></blockquote><p>[Mon Apr 29 10:38:01 2019]
Finished job 17.
13 of 33 steps (39%) done</p><p>[Mon Apr 29 10:38:01 2019]
rule map_reads:
input: trimmed/B-2.fastq.gz
output: mapped/B-2.sorted.bam
log: logs/bwa_mem/B-2.log
jobid: 22
wildcards: sample=B, unit=2
threads: 8</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpeg4eujj6.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/332db904</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">(bwa mem -t 8 -R '@RG\tID:B\tSM:B\tPL:ILLUMINA' data/ref/genome.chr21.fa trimmed/B-2.fastq.gz | samtools sort -T mapped/B-2.sorted.tmp -o mapped/B-2.sorted.bam -) 2> logs/bwa_mem/B-2.log</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 40px;"></div><div class="CodeMirror-gutters" style="display: none; height: 40px;"></div></div></div></pre><blockquote><p>Removing temporary output file trimmed/B-2.fastq.gz.</p></blockquote><p>[Mon Apr 29 10:38:04 2019]
Finished job 22.
14 of 33 steps (42%) done</p><p>[Mon Apr 29 10:38:04 2019]
rule samtools_stats:
input: recal/A-1.bam
output: qc/samtools-stats/A-1.txt
log: logs/samtools-stats/A-1.log
jobid: 5
wildcards: sample=A, unit=1</p><p>[Mon Apr 29 10:38:04 2019]
rule mark_duplicates:
input: mapped/B-2.sorted.bam
output: dedup/B-2.bam, qc/dedup/B-2.metrics.txt
log: logs/picard/dedup/B-2.log
jobid: 13
wildcards: sample=B, unit=2</p><p>[Mon Apr 29 10:38:04 2019]
rule call_variants:
input: recal/A-1.bam, data/ref/genome.chr21.fa, data/ref/dbsnp.vcf.gz
output: called/A.21.g.vcf.gz
log: logs/gatk/haplotypecaller/A.21.log
jobid: 31
wildcards: sample=A, contig=21</p><p>/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpsulq8zu5.wrapper.py
python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmphcnmlo_b.wrapper.py
python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpdgzoeza1.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/931cfa38
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/c70824eb</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">picard MarkDuplicates REMOVE_DUPLICATES=true INPUT=mapped/B-2.sorted.bam OUTPUT=dedup/B-2.bam METRICS_FILE=qc/dedup/B-2.metrics.txt &> logs/picard/dedup/B-2.log</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk HaplotypeCaller --intervals 21 -R data/ref/genome.chr21.fa -I recal/A-1.bam -ERC GVCF -O called/A.21.g.vcf.gz --dbsnp data/ref/dbsnp.vcf.gz > logs/gatk/haplotypecaller/A.21.log 2>&1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">samtools stats recal/A-1.bam > qc/samtools-stats/A-1.txt 2> logs/samtools-stats/A-1.log</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 140px;"></div><div class="CodeMirror-gutters" style="display: none; height: 140px;"></div></div></div></pre><p>[Mon Apr 29 10:38:06 2019]
Finished job 5.
15 of 33 steps (45%) done</p><blockquote><p>Removing temporary output file mapped/B-2.sorted.bam.</p></blockquote><p>[Mon Apr 29 10:38:07 2019]
Finished job 13.
16 of 33 steps (48%) done</p><p>[Mon Apr 29 10:38:07 2019]
rule recalibrate_base_qualities:
input: dedup/B-2.bam, data/ref/genome.chr21.fa, data/ref/dbsnp.vcf.gz
output: recal/B-2.bam
log: logs/gatk/bqsr/B-2.log
jobid: 21
wildcards: sample=B, unit=2</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpb0yjnxhs.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk BaseRecalibrator -R data/ref/genome.chr21.fa -I dedup/B-2.bam -O /tmp/tmpis2ryhs1/recal_table.grp --known-sites data/ref/dbsnp.vcf.gz > logs/gatk/bqsr/B-2.log 2>&1</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk ApplyBQSR -R data/ref/genome.chr21.fa -I dedup/B-2.bam --bqsr-recal-file /tmp/tmpis2ryhs1/recal_table.grp -O recal/B-2.bam >> logs/gatk/bqsr/B-2.log 2>&1</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 120px;"></div><div class="CodeMirror-gutters" style="display: none; height: 120px;"></div></div></div></pre><blockquote><p>Write-protecting output file recal/B-2.bam.
Removing temporary output file dedup/B-2.bam.</p></blockquote><p>[Mon Apr 29 10:38:17 2019]
Finished job 21.
17 of 33 steps (52%) done</p><p>[Mon Apr 29 10:38:17 2019]
rule samtools_stats:
input: recal/B-2.bam
output: qc/samtools-stats/B-2.txt
log: logs/samtools-stats/B-2.log
jobid: 11
wildcards: sample=B, unit=2</p><p>[Mon Apr 29 10:38:17 2019]
rule call_variants:
input: recal/B-1.bam, recal/B-2.bam, data/ref/genome.chr21.fa, data/ref/dbsnp.vcf.gz
output: called/B.21.g.vcf.gz
log: logs/gatk/haplotypecaller/B.21.log
jobid: 32
wildcards: sample=B, contig=21</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmptu4i6edy.wrapper.py
/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpmhcgf_1k.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/c70824eb
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk HaplotypeCaller --intervals 21 -R data/ref/genome.chr21.fa -I recal/B-1.bam -I recal/B-2.bam -ERC GVCF -O called/B.21.g.vcf.gz --dbsnp data/ref/dbsnp.vcf.gz > logs/gatk/haplotypecaller/B.21.log 2>&1</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">samtools stats recal/B-2.bam > qc/samtools-stats/B-2.txt 2> logs/samtools-stats/B-2.log</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 100px;"></div><div class="CodeMirror-gutters" style="display: none; height: 100px;"></div></div></div></pre><p>[Mon Apr 29 10:38:19 2019]
Finished job 11.
18 of 33 steps (55%) done</p><blockquote><p>Write-protecting output file called/A.21.g.vcf.gz.</p></blockquote><p>[Mon Apr 29 10:39:05 2019]
Finished job 31.
19 of 33 steps (58%) done</p><blockquote><p>Write-protecting output file called/B.21.g.vcf.gz.</p></blockquote><p>[Mon Apr 29 10:39:19 2019]
Finished job 32.
20 of 33 steps (61%) done</p><p>[Mon Apr 29 10:39:19 2019]
rule combine_calls:
input: data/ref/genome.chr21.fa, called/A.21.g.vcf.gz, called/B.21.g.vcf.gz
output: called/all.21.g.vcf.gz
log: logs/gatk/combinegvcfs.21.log
jobid: 30
wildcards: contig=21</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpxf7pu2_4.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk CombineGVCFs -V called/A.21.g.vcf.gz -V called/B.21.g.vcf.gz -R data/ref/genome.chr21.fa -O called/all.21.g.vcf.gz > logs/gatk/combinegvcfs.21.log 2>&1</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 40px;"></div><div class="CodeMirror-gutters" style="display: none; height: 40px;"></div></div></div></pre><p>[Mon Apr 29 10:39:26 2019]
Finished job 30.
21 of 33 steps (64%) done</p><p>[Mon Apr 29 10:39:26 2019]
rule genotype_variants:
input: data/ref/genome.chr21.fa, called/all.21.g.vcf.gz
output: genotyped/all.21.vcf.gz
log: logs/gatk/genotypegvcfs.21.log
jobid: 29
wildcards: contig=21</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpwchpfpyy.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk GenotypeGVCFs -V called/all.21.g.vcf.gz -R data/ref/genome.chr21.fa -O genotyped/all.21.vcf.gz > logs/gatk/genotypegvcfs.21.log 2>&1</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 40px;"></div><div class="CodeMirror-gutters" style="display: none; height: 40px;"></div></div></div></pre><p>[Mon Apr 29 10:39:32 2019]
Finished job 29.
22 of 33 steps (67%) done</p><p>[Mon Apr 29 10:39:32 2019]
rule merge_variants:
input: genotyped/all.21.vcf.gz
output: genotyped/all.vcf.gz
log: logs/picard/merge-genotyped.log
jobid: 28</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpklx955xr.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/931cfa38</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">picard MergeVcfs INPUT=genotyped/all.21.vcf.gz OUTPUT=genotyped/all.vcf.gz 2> logs/picard/merge-genotyped.log</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 40px;"></div><div class="CodeMirror-gutters" style="display: none; height: 40px;"></div></div></div></pre><blockquote><p>Removing temporary output file genotyped/all.21.vcf.gz.</p></blockquote><p>[Mon Apr 29 10:39:35 2019]
Finished job 28.
23 of 33 steps (70%) done</p><p>[Mon Apr 29 10:39:35 2019]
rule select_calls:
input: data/ref/genome.chr21.fa, genotyped/all.vcf.gz
output: filtered/all.snvs.vcf.gz
log: logs/gatk/selectvariants/snvs.log
jobid: 23
wildcards: vartype=snvs</p><p>[Mon Apr 29 10:39:35 2019]
rule select_calls:
input: data/ref/genome.chr21.fa, genotyped/all.vcf.gz
output: filtered/all.indels.vcf.gz
log: logs/gatk/selectvariants/indels.log
jobid: 24
wildcards: vartype=indels</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpscualt3h.wrapper.py
python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpl6rfir0b.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk SelectVariants -R data/ref/genome.chr21.fa -V genotyped/all.vcf.gz --select-type-to-include SNP -O filtered/all.snvs.vcf.gz > logs/gatk/selectvariants/snvs.log 2>&1</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk SelectVariants -R data/ref/genome.chr21.fa -V genotyped/all.vcf.gz --select-type-to-include INDEL -O filtered/all.indels.vcf.gz > logs/gatk/selectvariants/indels.log 2>&1</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 100px;"></div><div class="CodeMirror-gutters" style="display: none; height: 100px;"></div></div></div></pre><p>[Mon Apr 29 10:39:40 2019]
Finished job 24.
24 of 33 steps (73%) done</p><p>[Mon Apr 29 10:39:40 2019]
rule hard_filter_calls:
input: data/ref/genome.chr21.fa, filtered/all.indels.vcf.gz
output: filtered/all.indels.hardfiltered.vcf.gz
log: logs/gatk/variantfiltration/indels.log
jobid: 16
wildcards: vartype=indels</p><p>[Mon Apr 29 10:39:40 2019]
Finished job 23.
25 of 33 steps (76%) done</p><p>[Mon Apr 29 10:39:40 2019]
rule hard_filter_calls:
input: data/ref/genome.chr21.fa, filtered/all.snvs.vcf.gz
output: filtered/all.snvs.hardfiltered.vcf.gz
log: logs/gatk/variantfiltration/snvs.log
jobid: 15
wildcards: vartype=snvs</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmp0gwimrlg.wrapper.py
python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmp335528m0.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/21f0a586</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk VariantFiltration -R data/ref/genome.chr21.fa -V filtered/all.indels.vcf.gz --filter-name snv-hard-filter --filter-expression 'QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0' -O filtered/all.indels.hardfiltered.vcf.gz > logs/gatk/variantfiltration/indels.log 2>&1</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">gatk VariantFiltration -R data/ref/genome.chr21.fa -V filtered/all.snvs.vcf.gz --filter-name snv-hard-filter --filter-expression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0' -O filtered/all.snvs.hardfiltered.vcf.gz > logs/gatk/variantfiltration/snvs.log 2>&1</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 160px;"></div><div class="CodeMirror-gutters" style="display: none; height: 160px;"></div></div></div></pre><blockquote><p>Removing temporary output file filtered/all.indels.vcf.gz.</p></blockquote><p>[Mon Apr 29 10:39:45 2019]
Finished job 16.
26 of 33 steps (79%) done</p><blockquote><p>Removing temporary output file filtered/all.snvs.vcf.gz.</p></blockquote><p>[Mon Apr 29 10:39:45 2019]
Finished job 15.
27 of 33 steps (82%) done</p><p>[Mon Apr 29 10:39:45 2019]
rule merge_calls:
input: filtered/all.snvs.hardfiltered.vcf.gz, filtered/all.indels.hardfiltered.vcf.gz
output: filtered/all.vcf.gz
log: logs/picard/merge-filtered.log
jobid: 4</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpc6ke25oy.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/931cfa38</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">picard MergeVcfs INPUT=filtered/all.snvs.hardfiltered.vcf.gz INPUT=filtered/all.indels.hardfiltered.vcf.gz OUTPUT=filtered/all.vcf.gz 2> logs/picard/merge-filtered.log</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 60px;"></div><div class="CodeMirror-gutters" style="display: none; height: 60px;"></div></div></div></pre><blockquote><p>Removing temporary output file filtered/all.snvs.hardfiltered.vcf.gz.
Removing temporary output file filtered/all.indels.hardfiltered.vcf.gz.</p></blockquote><p>[Mon Apr 29 10:39:48 2019]
Finished job 4.
28 of 33 steps (85%) done</p><p>[Mon Apr 29 10:39:48 2019]
rule snpeff:
input: filtered/all.vcf.gz
output: annotated/all.vcf.gz, snpeff/all.csv
log: logs/snpeff.log
jobid: 1</p><p>/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpizt_itqb.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/9a672934</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">(snpEff -noStats -csvStats snpeff/all.csv -Xmx6g GRCh38.86 filtered/all.vcf.gz > annotated/all.vcf.gz) 2> logs/snpeff.log</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 40px;"></div><div class="CodeMirror-gutters" style="display: none; height: 40px;"></div></div></div></pre><p>[Mon Apr 29 10:40:23 2019]
Finished job 1.
29 of 33 steps (88%) done</p><p>[Mon Apr 29 10:40:23 2019]
rule vcf_to_tsv:
input: annotated/all.vcf.gz
output: tables/calls.tsv.gz
jobid: 14</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4.16669px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">bcftools view --apply-filters PASS --output-type u annotated/all.vcf.gz | rbt vcf-to-txt -g --fmt DP AD --info ANN | gzip > tables/calls.tsv.gz</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 40px;"></div><div class="CodeMirror-gutters" style="display: none; height: 40px;"></div></div></div></pre><p>[Mon Apr 29 10:40:23 2019]
rule multiqc:
input: qc/samtools-stats/A-1.txt, qc/fastqc/A-1.zip, qc/dedup/A-1.metrics.txt, qc/samtools-stats/B-1.txt, qc/fastqc/B-1.zip, qc/dedup/B-1.metrics.txt, qc/samtools-stats/B-2.txt, qc/fastqc/B-2.zip, qc/dedup/B-2.metrics.txt, snpeff/all.csv
output: qc/multiqc.html
log: logs/multiqc.log
jobid: 2</p><p>WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/783643b9
[Mon Apr 29 10:40:24 2019]
Finished job 14.
30 of 33 steps (91%) done</p><p>[Mon Apr 29 10:40:24 2019]
rule plot_stats:
input: tables/calls.tsv.gz
output: plots/depths.svg, plots/allele-freqs.svg
jobid: 3</p><p>python /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmpbp1vlae6.plot-depths.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/4c3018c1
Conda environment defines Python version < 3.5. Using Python of the master process to execute script. Note that this cannot be avoided, because the script uses data structures from Snakemake which are Python >=3.5 only.
/home/alper/miniconda3/bin/python3.7 /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/scripts/tmp4ctdm_gu.wrapper.py
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Activating conda environment: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/conda/b822cd76
/home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/scripts/plot-depths.py:11: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded md-focus" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap CodeMirror-focused" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 19.5835px; left: 173.333px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">multiqc --force -o qc -n multiqc.html qc/samtools-stats qc/dedup snpeff qc/fastqc > logs/multiqc.log 2>&1</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 40px;"></div><div class="CodeMirror-gutters" style="display: none; height: 40px;"></div></div></div></pre><p>[Mon Apr 29 10:40:25 2019]
Finished job 3.
31 of 33 steps (94%) done
[Mon Apr 29 10:40:28 2019]
Finished job 2.
32 of 33 steps (97%) done</p><p>[Mon Apr 29 10:40:28 2019]
localrule all:
input: annotated/all.vcf.gz, qc/multiqc.html, plots/depths.svg, plots/allele-freqs.svg
jobid: 0</p><p>[Mon Apr 29 10:40:28 2019]
Finished job 0.
33 of 33 steps (100%) done
Complete log: /home/alper/tmp/snakemake-dna-seq-gatk-variant-calling-1.0.1/.snakemake/log/2019-04-29T103714.426290.snakemake.log</p></div>
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