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Add GATK Depth of coverage, Read Group ID to Bowtie runs and Picard S…
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@alipirani88
alipirani88 committed Jul 28, 2021
1 parent 0c6c33c commit 6d0b417
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Showing 103 changed files with 2,214 additions and 192 deletions.
219 changes: 179 additions & 40 deletions .idea/workspace.xml
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112 changes: 112 additions & 0 deletions .snakemake/log/2021-07-28T100010.461526.snakemake.log
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Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
-------------------- ------- ------------- -------------
GATK_DepthofCoverage 2 1 1
GATK_MarkDuplicates 2 1 1
all 1 1 1
bowtie2Align 2 4 4
freebayes 2 1 1
samtools_index 2 1 1
total 11 1 4

Select jobs to execute...

[Wed Jul 28 10:00:13 2021]
rule bowtie2Align:
input: trimmed/A_R1_001.fastq.gz, trimmed/A_R2_001.fastq.gz, trimmed/A_R1_unpaired.fastq.gz, trimmed/A_R2_unpaired.fastq.gz, resources/Aus0004.fasta.1.bt2
output: mapped/A_aln.sam, mapped/A_aln.bam, mapped/A_aln_sort.bam
log: logs/bowtie2/A.log
jobid: 3
wildcards: sample=A
threads: 4
resources: tmpdir=/tmp

Removing temporary output file mapped/A_aln.sam.
Removing temporary output file mapped/A_aln.bam.
[Wed Jul 28 10:02:11 2021]
Finished job 3.
1 of 11 steps (9%) done
Select jobs to execute...

[Wed Jul 28 10:02:11 2021]
rule bowtie2Align:
input: trimmed/B_R1_001.fastq.gz, trimmed/B_R2_001.fastq.gz, trimmed/B_R1_unpaired.fastq.gz, trimmed/B_R2_unpaired.fastq.gz, resources/Aus0004.fasta.1.bt2
output: mapped/B_aln.sam, mapped/B_aln.bam, mapped/B_aln_sort.bam
log: logs/bowtie2/B.log
jobid: 8
wildcards: sample=B
threads: 4
resources: tmpdir=/tmp

Removing temporary output file mapped/B_aln.sam.
Removing temporary output file mapped/B_aln.bam.
[Wed Jul 28 10:04:12 2021]
Finished job 8.
2 of 11 steps (18%) done
Select jobs to execute...

[Wed Jul 28 10:04:12 2021]
rule GATK_MarkDuplicates:
input: mapped/B_aln_sort.bam
output: DedupReads/B_aln_marked.bam, DedupReads/B_marked_dup_metrics.txt
log: logs/gatk/B_GATK_MarkDuplicates.log
jobid: 7
wildcards: sample=B
resources: tmpdir=/tmp


[Wed Jul 28 10:04:12 2021]
rule GATK_MarkDuplicates:
input: mapped/A_aln_sort.bam
output: DedupReads/A_aln_marked.bam, DedupReads/A_marked_dup_metrics.txt
log: logs/gatk/A_GATK_MarkDuplicates.log
jobid: 2
wildcards: sample=A
resources: tmpdir=/tmp

[Wed Jul 28 10:05:07 2021]
Finished job 7.
3 of 11 steps (27%) done
Select jobs to execute...

[Wed Jul 28 10:05:07 2021]
rule samtools_index:
input: DedupReads/B_aln_marked.bam
output: DedupReads/B_aln_marked.bam.bai
log: logs/samtools/B_samtools.log
jobid: 6
wildcards: sample=B
resources: tmpdir=/tmp


[Wed Jul 28 10:05:07 2021]
rule GATK_DepthofCoverage:
input: DedupReads/B_aln_marked.bam, resources/Aus0004.fasta
output: DedupReads/B_depth_of_coverage
log: logs/gatk/B_GATK_DepthofCoverage.log
jobid: 12
wildcards: sample=B
resources: tmpdir=/tmp

[Wed Jul 28 10:05:07 2021]
Error in rule GATK_DepthofCoverage:
jobid: 12
output: DedupReads/B_depth_of_coverage
log: logs/gatk/B_GATK_DepthofCoverage.log (check log file(s) for error message)
shell:
java -Xmx5G -jar /bin/GenomeAnalysisTK.jar -T DepthOfCoverage -R resources/Aus0004.fasta -o DedupReads/B_depth_of_coverage -I DedupReads/B_aln_marked.bam --summaryCoverageThreshold 1 --summaryCoverageThreshold 2 --summaryCoverageThreshold 3 --summaryCoverageThreshold 4 --summaryCoverageThreshold 5 --summaryCoverageThreshold 6 --summaryCoverageThreshold 7 --summaryCoverageThreshold 8 --summaryCoverageThreshold 9 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 25 --ignoreDeletionSites 2>logs/gatk/B_GATK_DepthofCoverage.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Jul 28 10:05:07 2021]
Finished job 2.
4 of 11 steps (36%) done
[Wed Jul 28 10:05:11 2021]
Finished job 6.
5 of 11 steps (45%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /nfs/esnitkin/Github/samosa/.snakemake/log/2021-07-28T100010.461526.snakemake.log
88 changes: 88 additions & 0 deletions .snakemake/log/2021-07-28T101646.627905.snakemake.log
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Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
-------------------- ------- ------------- -------------
GATK_DepthofCoverage 2 1 1
all 1 1 1
freebayes 2 1 1
samtools_index 1 1 1
total 6 1 1

Select jobs to execute...

[Wed Jul 28 10:16:48 2021]
rule GATK_DepthofCoverage:
input: DedupReads/A_aln_marked.bam, resources/Aus0004.fasta
output: DedupReads/A_depth_of_coverage
log: logs/gatk/A_GATK_DepthofCoverage.log
jobid: 11
wildcards: sample=A
resources: tmpdir=/tmp


[Wed Jul 28 10:16:48 2021]
rule GATK_DepthofCoverage:
input: DedupReads/B_aln_marked.bam, resources/Aus0004.fasta
output: DedupReads/B_depth_of_coverage
log: logs/gatk/B_GATK_DepthofCoverage.log
jobid: 12
wildcards: sample=B
resources: tmpdir=/tmp


[Wed Jul 28 10:16:48 2021]
rule freebayes:
input: DedupReads/B_aln_marked.bam, DedupReads/B_aln_marked.bam.bai, resources/Aus0004.fasta.fai, resources/Aus0004.fasta
output: freebayes/B_raw.vcf
log: logs/freebayes/B_freebayes.log
jobid: 14
wildcards: sample=B
resources: tmpdir=/tmp

[Wed Jul 28 10:16:48 2021]
Error in rule GATK_DepthofCoverage:
jobid: 11
output: DedupReads/A_depth_of_coverage
log: logs/gatk/A_GATK_DepthofCoverage.log (check log file(s) for error message)
shell:
java -Xmx5G -jar /bin/GenomeAnalysisTK.jar -T DepthOfCoverage -R resources/Aus0004.fasta -o DedupReads/A_depth_of_coverage -I DedupReads/A_aln_marked.bam --summaryCoverageThreshold 1 --summaryCoverageThreshold 2 --summaryCoverageThreshold 3 --summaryCoverageThreshold 4 --summaryCoverageThreshold 5 --summaryCoverageThreshold 6 --summaryCoverageThreshold 7 --summaryCoverageThreshold 8 --summaryCoverageThreshold 9 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 25 --ignoreDeletionSites 2>logs/gatk/A_GATK_DepthofCoverage.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)


[Wed Jul 28 10:16:48 2021]
rule samtools_index:
input: DedupReads/A_aln_marked.bam
output: DedupReads/A_aln_marked.bam.bai
log: logs/samtools/A_samtools.log
jobid: 1
wildcards: sample=A
resources: tmpdir=/tmp

[Wed Jul 28 10:16:48 2021]
Error in rule GATK_DepthofCoverage:
jobid: 12
output: DedupReads/B_depth_of_coverage
log: logs/gatk/B_GATK_DepthofCoverage.log (check log file(s) for error message)
shell:
java -Xmx5G -jar /bin/GenomeAnalysisTK.jar -T DepthOfCoverage -R resources/Aus0004.fasta -o DedupReads/B_depth_of_coverage -I DedupReads/B_aln_marked.bam --summaryCoverageThreshold 1 --summaryCoverageThreshold 2 --summaryCoverageThreshold 3 --summaryCoverageThreshold 4 --summaryCoverageThreshold 5 --summaryCoverageThreshold 6 --summaryCoverageThreshold 7 --summaryCoverageThreshold 8 --summaryCoverageThreshold 9 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 25 --ignoreDeletionSites 2>logs/gatk/B_GATK_DepthofCoverage.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Jul 28 10:16:52 2021]
Finished job 1.
1 of 6 steps (17%) done
Terminating processes on user request, this might take some time.
[Wed Jul 28 10:17:00 2021]
Error in rule freebayes:
jobid: 14
output: freebayes/B_raw.vcf
log: logs/freebayes/B_freebayes.log (check log file(s) for error message)
shell:
freebayes-parallel <(fasta_generate_regions.py resources/Aus0004.fasta.fai 100000) 4 -f resources/Aus0004.fasta --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic DedupReads/B_aln_marked.bam > freebayes/B_raw.vcf
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job freebayes since they might be corrupted:
freebayes/B_raw.vcf
Complete log: /nfs/esnitkin/Github/samosa/.snakemake/log/2021-07-28T101646.627905.snakemake.log
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T102613.554535.snakemake.log
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SyntaxError:
Not all output, log and benchmark files of rule GATK_DepthofCoverage contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 25, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 23, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T102636.425539.snakemake.log
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@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule GATK_DepthofCoverage contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 25, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 22, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T102734.178021.snakemake.log
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@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule GATK_DepthofCoverage contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 25, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 22, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103048.770051.snakemake.log
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@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule GATK_DepthofCoverage contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 26, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 22, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103131.998322.snakemake.log
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@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule GATK_DepthofCoverage contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 26, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 22, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103211.502067.snakemake.log
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@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule GATK_DepthofCoverage contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 26, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 22, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103240.519972.snakemake.log
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@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule GATK_DepthofCoverage contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 26, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 22, in <module>
5 changes: 5 additions & 0 deletions .snakemake/log/2021-07-28T103256.230785.snakemake.log
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Building DAG of jobs...
MissingInputException in line 11 of /nfs/esnitkin/Github/samosa/workflow/Snakefile:
Missing input files for rule all:
DedupReads/A_depth_of_coverage
DedupReads/B_depth_of_coverage
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103347.731469.snakemake.log
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@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule GATK_DepthofCoverage contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 26, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 24, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103503.254358.snakemake.log
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@@ -0,0 +1,4 @@
Building DAG of jobs...
WildcardError in line 12 of /nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk:
Wildcards in input files cannot be determined from output files:
'sample'
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103808.678368.snakemake.log
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@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule picard_SeqDict contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 27, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 20, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103835.045477.snakemake.log
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule picard_SeqDict contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 27, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 20, in <module>
4 changes: 4 additions & 0 deletions .snakemake/log/2021-07-28T103847.252217.snakemake.log
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
SyntaxError:
Not all output, log and benchmark files of rule picard_SeqDict contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
File "/nfs/esnitkin/Github/samosa/workflow/Snakefile", line 27, in <module>
File "/nfs/esnitkin/Github/samosa/workflow/rules/gatk.smk", line 20, in <module>
12 changes: 12 additions & 0 deletions .snakemake/log/2021-07-28T103901.911938.snakemake.log
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@@ -0,0 +1,12 @@
Building DAG of jobs...
AmbiguousRuleException:
Rules GATK_DepthofCoverage and picard_SeqDict are ambiguous for the file resources/Aus0004.dict.
Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
Wildcards:
GATK_DepthofCoverage:
picard_SeqDict:
Expected input files:
GATK_DepthofCoverage: resources/Aus0004.fasta
picard_SeqDict: resources/Aus0004.fastaExpected output files:
GATK_DepthofCoverage: resources/Aus0004.dict
picard_SeqDict: resources/Aus0004.dict
108 changes: 108 additions & 0 deletions .snakemake/log/2021-07-28T104048.062837.snakemake.log
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@@ -0,0 +1,108 @@
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
-------------------- ------- ------------- -------------
GATK_DepthofCoverage 2 1 1
all 1 1 1
freebayes 2 1 1
picard_SeqDict 1 1 1
total 6 1 1

Select jobs to execute...

[Wed Jul 28 10:40:49 2021]
rule freebayes:
input: DedupReads/B_aln_marked.bam, DedupReads/B_aln_marked.bam.bai, resources/Aus0004.fasta.fai, resources/Aus0004.fasta
output: freebayes/B_raw.vcf
log: logs/freebayes/B_freebayes.log
jobid: 15
wildcards: sample=B
resources: tmpdir=/tmp


[Wed Jul 28 10:40:49 2021]
rule picard_SeqDict:
input: resources/Aus0004.fasta
output: resources/Aus0004.dict
jobid: 12
resources: tmpdir=/tmp


[Wed Jul 28 10:40:49 2021]
rule freebayes:
input: DedupReads/A_aln_marked.bam, DedupReads/A_aln_marked.bam.bai, resources/Aus0004.fasta.fai, resources/Aus0004.fasta
output: freebayes/A_raw.vcf
log: logs/freebayes/A_freebayes.log
jobid: 14
wildcards: sample=A
resources: tmpdir=/tmp

[Wed Jul 28 10:40:50 2021]
Finished job 12.
1 of 6 steps (17%) done
Select jobs to execute...

[Wed Jul 28 10:40:50 2021]
rule GATK_DepthofCoverage:
input: DedupReads/A_aln_marked.bam, resources/Aus0004.fasta, resources/Aus0004.dict
output: DedupReads/A_depth_of_coverage
log: logs/gatk/A_GATK_DepthofCoverage.log
jobid: 11
wildcards: sample=A
resources: tmpdir=/tmp


[Wed Jul 28 10:40:50 2021]
rule GATK_DepthofCoverage:
input: DedupReads/B_aln_marked.bam, resources/Aus0004.fasta, resources/Aus0004.dict
output: DedupReads/B_depth_of_coverage
log: logs/gatk/B_GATK_DepthofCoverage.log
jobid: 13
wildcards: sample=B
resources: tmpdir=/tmp

[Wed Jul 28 10:40:50 2021]
Error in rule GATK_DepthofCoverage:
jobid: 11
output: DedupReads/A_depth_of_coverage
log: logs/gatk/A_GATK_DepthofCoverage.log (check log file(s) for error message)
shell:
java -Xmx5G -jar /bin/GenomeAnalysisTK.jar -T DepthOfCoverage -R resources/Aus0004.fasta -o DedupReads/A_depth_of_coverage -I DedupReads/A_aln_marked.bam --summaryCoverageThreshold 1 --summaryCoverageThreshold 2 --summaryCoverageThreshold 3 --summaryCoverageThreshold 4 --summaryCoverageThreshold 5 --summaryCoverageThreshold 6 --summaryCoverageThreshold 7 --summaryCoverageThreshold 8 --summaryCoverageThreshold 9 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 25 --ignoreDeletionSites 2>logs/gatk/A_GATK_DepthofCoverage.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Jul 28 10:40:50 2021]
Error in rule GATK_DepthofCoverage:
jobid: 13
output: DedupReads/B_depth_of_coverage
log: logs/gatk/B_GATK_DepthofCoverage.log (check log file(s) for error message)
shell:
java -Xmx5G -jar /bin/GenomeAnalysisTK.jar -T DepthOfCoverage -R resources/Aus0004.fasta -o DedupReads/B_depth_of_coverage -I DedupReads/B_aln_marked.bam --summaryCoverageThreshold 1 --summaryCoverageThreshold 2 --summaryCoverageThreshold 3 --summaryCoverageThreshold 4 --summaryCoverageThreshold 5 --summaryCoverageThreshold 6 --summaryCoverageThreshold 7 --summaryCoverageThreshold 8 --summaryCoverageThreshold 9 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 25 --ignoreDeletionSites 2>logs/gatk/B_GATK_DepthofCoverage.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Terminating processes on user request, this might take some time.
[Wed Jul 28 10:40:58 2021]
Error in rule freebayes:
jobid: 14
output: freebayes/A_raw.vcf
[Wed Jul 28 10:40:58 2021]
log: logs/freebayes/A_freebayes.log (check log file(s) for error message)
Error in rule freebayes:
shell:
freebayes-parallel <(fasta_generate_regions.py resources/Aus0004.fasta.fai 100000) 4 -f resources/Aus0004.fasta --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic DedupReads/A_aln_marked.bam > freebayes/A_raw.vcf
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
jobid: 15

output: freebayes/B_raw.vcf
log: logs/freebayes/B_freebayes.log (check log file(s) for error message)
shell:
freebayes-parallel <(fasta_generate_regions.py resources/Aus0004.fasta.fai 100000) 4 -f resources/Aus0004.fasta --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic DedupReads/B_aln_marked.bam > freebayes/B_raw.vcf
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job freebayes since they might be corrupted:
freebayes/A_raw.vcf
Removing output files of failed job freebayes since they might be corrupted:
freebayes/B_raw.vcf
Complete log: /nfs/esnitkin/Github/samosa/.snakemake/log/2021-07-28T104048.062837.snakemake.log
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