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3477 lines (2801 loc) · 496 KB
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[-] Unloading python 3.7 ...
[+] Loading python 3.7 ...
[-] Unloading snakemake 5.24.1
[+] Loading snakemake 5.24.1
[+] Loading singularity 3.8.0 on cn2289
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 500
Job counts:
count jobs
1 all
1 create_nfragments_table
16 get_nfragments_json
32 get_split_reads
16 htseq
16 split_bam_by_mutation
82
[Fri Jul 23 12:16:08 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam.flagstat
jobid: 91
wildcards: sample=SRA_labeled_2
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/SRA_labeled_2.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/SRA_labeled_2.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.plus.bam -o /dev/shm/SRA_labeled_2.mutated.plus.bam --readids /dev/shm/SRA_labeled_2.plus.readids -o2 /dev/shm/SRA_labeled_2.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.minus.bam -o /dev/shm/SRA_labeled_2.mutated.minus.bam --readids /dev/shm/SRA_labeled_2.minus.readids -o2 /dev/shm/SRA_labeled_2.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/SRA_labeled_2.mutated.bam /dev/shm/SRA_labeled_2.mutated.plus.bam /dev/shm/SRA_labeled_2.mutated.minus.bam && rm -f /dev/shm/SRA_labeled_2.mutated.plus.bam /dev/shm/SRA_labeled_2.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam /dev/shm/SRA_labeled_2.mutated.bam && rm -f /dev/shm/SRA_labeled_2.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/SRA_labeled_2.unmutated.bam /dev/shm/SRA_labeled_2.unmutated.plus.bam /dev/shm/SRA_labeled_2.unmutated.minus.bam && rm -f /dev/shm/SRA_labeled_2.unmutated.plus.bam /dev/shm/SRA_labeled_2.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam /dev/shm/SRA_labeled_2.unmutated.bam && rm -f /dev/shm/SRA_labeled_2.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam.flagstat
Submitted job 91 with external jobid '19834916'.
[Fri Jul 23 12:16:12 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam.flagstat
jobid: 93
wildcards: sample=SRA_unlabeled_2
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/SRA_unlabeled_2.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/SRA_unlabeled_2.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.plus.bam -o /dev/shm/SRA_unlabeled_2.mutated.plus.bam --readids /dev/shm/SRA_unlabeled_2.plus.readids -o2 /dev/shm/SRA_unlabeled_2.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.minus.bam -o /dev/shm/SRA_unlabeled_2.mutated.minus.bam --readids /dev/shm/SRA_unlabeled_2.minus.readids -o2 /dev/shm/SRA_unlabeled_2.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/SRA_unlabeled_2.mutated.bam /dev/shm/SRA_unlabeled_2.mutated.plus.bam /dev/shm/SRA_unlabeled_2.mutated.minus.bam && rm -f /dev/shm/SRA_unlabeled_2.mutated.plus.bam /dev/shm/SRA_unlabeled_2.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /dev/shm/SRA_unlabeled_2.mutated.bam && rm -f /dev/shm/SRA_unlabeled_2.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/SRA_unlabeled_2.unmutated.bam /dev/shm/SRA_unlabeled_2.unmutated.plus.bam /dev/shm/SRA_unlabeled_2.unmutated.minus.bam && rm -f /dev/shm/SRA_unlabeled_2.unmutated.plus.bam /dev/shm/SRA_unlabeled_2.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /dev/shm/SRA_unlabeled_2.unmutated.bam && rm -f /dev/shm/SRA_unlabeled_2.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam.flagstat
Submitted job 93 with external jobid '19834922'.
[Fri Jul 23 12:16:18 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep2_unlabeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep2_unlabeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep2_unlabeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep2_unlabeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.unmutated.bam.flagstat
jobid: 97
wildcards: sample=WT4_techrep2_unlabeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep2_unlabeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep2_unlabeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep2_unlabeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/WT4_techrep2_unlabeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep2_unlabeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep2_unlabeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep2_unlabeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/WT4_techrep2_unlabeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep2_unlabeled.plus.bam -o /dev/shm/WT4_techrep2_unlabeled.mutated.plus.bam --readids /dev/shm/WT4_techrep2_unlabeled.plus.readids -o2 /dev/shm/WT4_techrep2_unlabeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep2_unlabeled.minus.bam -o /dev/shm/WT4_techrep2_unlabeled.mutated.minus.bam --readids /dev/shm/WT4_techrep2_unlabeled.minus.readids -o2 /dev/shm/WT4_techrep2_unlabeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/WT4_techrep2_unlabeled.mutated.bam /dev/shm/WT4_techrep2_unlabeled.mutated.plus.bam /dev/shm/WT4_techrep2_unlabeled.mutated.minus.bam && rm -f /dev/shm/WT4_techrep2_unlabeled.mutated.plus.bam /dev/shm/WT4_techrep2_unlabeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.mutated.bam /dev/shm/WT4_techrep2_unlabeled.mutated.bam && rm -f /dev/shm/WT4_techrep2_unlabeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/WT4_techrep2_unlabeled.unmutated.bam /dev/shm/WT4_techrep2_unlabeled.unmutated.plus.bam /dev/shm/WT4_techrep2_unlabeled.unmutated.minus.bam && rm -f /dev/shm/WT4_techrep2_unlabeled.unmutated.plus.bam /dev/shm/WT4_techrep2_unlabeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.unmutated.bam /dev/shm/WT4_techrep2_unlabeled.unmutated.bam && rm -f /dev/shm/WT4_techrep2_unlabeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep2_unlabeled.unmutated.bam.flagstat
Submitted job 97 with external jobid '19834927'.
[Fri Jul 23 12:16:24 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep1_unlabeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep1_unlabeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep1_unlabeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep1_unlabeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.unmutated.bam.flagstat
jobid: 94
wildcards: sample=KO1_techrep1_unlabeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep1_unlabeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep1_unlabeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep1_unlabeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/KO1_techrep1_unlabeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep1_unlabeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep1_unlabeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep1_unlabeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/KO1_techrep1_unlabeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep1_unlabeled.plus.bam -o /dev/shm/KO1_techrep1_unlabeled.mutated.plus.bam --readids /dev/shm/KO1_techrep1_unlabeled.plus.readids -o2 /dev/shm/KO1_techrep1_unlabeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep1_unlabeled.minus.bam -o /dev/shm/KO1_techrep1_unlabeled.mutated.minus.bam --readids /dev/shm/KO1_techrep1_unlabeled.minus.readids -o2 /dev/shm/KO1_techrep1_unlabeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/KO1_techrep1_unlabeled.mutated.bam /dev/shm/KO1_techrep1_unlabeled.mutated.plus.bam /dev/shm/KO1_techrep1_unlabeled.mutated.minus.bam && rm -f /dev/shm/KO1_techrep1_unlabeled.mutated.plus.bam /dev/shm/KO1_techrep1_unlabeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.mutated.bam /dev/shm/KO1_techrep1_unlabeled.mutated.bam && rm -f /dev/shm/KO1_techrep1_unlabeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/KO1_techrep1_unlabeled.unmutated.bam /dev/shm/KO1_techrep1_unlabeled.unmutated.plus.bam /dev/shm/KO1_techrep1_unlabeled.unmutated.minus.bam && rm -f /dev/shm/KO1_techrep1_unlabeled.unmutated.plus.bam /dev/shm/KO1_techrep1_unlabeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.unmutated.bam /dev/shm/KO1_techrep1_unlabeled.unmutated.bam && rm -f /dev/shm/KO1_techrep1_unlabeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep1_unlabeled.unmutated.bam.flagstat
Submitted job 94 with external jobid '19834936'.
[Fri Jul 23 12:16:30 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_4SU_labeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_4SU_labeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_4SU_labeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_4SU_labeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.unmutated.bam.flagstat
jobid: 82
wildcards: sample=KO1_4SU_labeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_4SU_labeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_4SU_labeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_4SU_labeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/KO1_4SU_labeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_4SU_labeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_4SU_labeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_4SU_labeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/KO1_4SU_labeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_4SU_labeled.plus.bam -o /dev/shm/KO1_4SU_labeled.mutated.plus.bam --readids /dev/shm/KO1_4SU_labeled.plus.readids -o2 /dev/shm/KO1_4SU_labeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_4SU_labeled.minus.bam -o /dev/shm/KO1_4SU_labeled.mutated.minus.bam --readids /dev/shm/KO1_4SU_labeled.minus.readids -o2 /dev/shm/KO1_4SU_labeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/KO1_4SU_labeled.mutated.bam /dev/shm/KO1_4SU_labeled.mutated.plus.bam /dev/shm/KO1_4SU_labeled.mutated.minus.bam && rm -f /dev/shm/KO1_4SU_labeled.mutated.plus.bam /dev/shm/KO1_4SU_labeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.mutated.bam /dev/shm/KO1_4SU_labeled.mutated.bam && rm -f /dev/shm/KO1_4SU_labeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/KO1_4SU_labeled.unmutated.bam /dev/shm/KO1_4SU_labeled.unmutated.plus.bam /dev/shm/KO1_4SU_labeled.unmutated.minus.bam && rm -f /dev/shm/KO1_4SU_labeled.unmutated.plus.bam /dev/shm/KO1_4SU_labeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.unmutated.bam /dev/shm/KO1_4SU_labeled.unmutated.bam && rm -f /dev/shm/KO1_4SU_labeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_4SU_labeled.unmutated.bam.flagstat
Submitted job 82 with external jobid '19834938'.
[Fri Jul 23 12:16:36 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep1_unlabeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep1_unlabeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep1_unlabeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep1_unlabeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.unmutated.bam.flagstat
jobid: 96
wildcards: sample=WT4_techrep1_unlabeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep1_unlabeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep1_unlabeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep1_unlabeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/WT4_techrep1_unlabeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep1_unlabeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_techrep1_unlabeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep1_unlabeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/WT4_techrep1_unlabeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep1_unlabeled.plus.bam -o /dev/shm/WT4_techrep1_unlabeled.mutated.plus.bam --readids /dev/shm/WT4_techrep1_unlabeled.plus.readids -o2 /dev/shm/WT4_techrep1_unlabeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_techrep1_unlabeled.minus.bam -o /dev/shm/WT4_techrep1_unlabeled.mutated.minus.bam --readids /dev/shm/WT4_techrep1_unlabeled.minus.readids -o2 /dev/shm/WT4_techrep1_unlabeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/WT4_techrep1_unlabeled.mutated.bam /dev/shm/WT4_techrep1_unlabeled.mutated.plus.bam /dev/shm/WT4_techrep1_unlabeled.mutated.minus.bam && rm -f /dev/shm/WT4_techrep1_unlabeled.mutated.plus.bam /dev/shm/WT4_techrep1_unlabeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.mutated.bam /dev/shm/WT4_techrep1_unlabeled.mutated.bam && rm -f /dev/shm/WT4_techrep1_unlabeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/WT4_techrep1_unlabeled.unmutated.bam /dev/shm/WT4_techrep1_unlabeled.unmutated.plus.bam /dev/shm/WT4_techrep1_unlabeled.unmutated.minus.bam && rm -f /dev/shm/WT4_techrep1_unlabeled.unmutated.plus.bam /dev/shm/WT4_techrep1_unlabeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.unmutated.bam /dev/shm/WT4_techrep1_unlabeled.unmutated.bam && rm -f /dev/shm/WT4_techrep1_unlabeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_techrep1_unlabeled.unmutated.bam.flagstat
Submitted job 96 with external jobid '19834942'.
[Fri Jul 23 12:16:40 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_4SU_labeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_4SU_labeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_4SU_labeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_4SU_labeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.unmutated.bam.flagstat
jobid: 84
wildcards: sample=KO8_4SU_labeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_4SU_labeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_4SU_labeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_4SU_labeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/KO8_4SU_labeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_4SU_labeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_4SU_labeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_4SU_labeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/KO8_4SU_labeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_4SU_labeled.plus.bam -o /dev/shm/KO8_4SU_labeled.mutated.plus.bam --readids /dev/shm/KO8_4SU_labeled.plus.readids -o2 /dev/shm/KO8_4SU_labeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_4SU_labeled.minus.bam -o /dev/shm/KO8_4SU_labeled.mutated.minus.bam --readids /dev/shm/KO8_4SU_labeled.minus.readids -o2 /dev/shm/KO8_4SU_labeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/KO8_4SU_labeled.mutated.bam /dev/shm/KO8_4SU_labeled.mutated.plus.bam /dev/shm/KO8_4SU_labeled.mutated.minus.bam && rm -f /dev/shm/KO8_4SU_labeled.mutated.plus.bam /dev/shm/KO8_4SU_labeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.mutated.bam /dev/shm/KO8_4SU_labeled.mutated.bam && rm -f /dev/shm/KO8_4SU_labeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/KO8_4SU_labeled.unmutated.bam /dev/shm/KO8_4SU_labeled.unmutated.plus.bam /dev/shm/KO8_4SU_labeled.unmutated.minus.bam && rm -f /dev/shm/KO8_4SU_labeled.unmutated.plus.bam /dev/shm/KO8_4SU_labeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.unmutated.bam /dev/shm/KO8_4SU_labeled.unmutated.bam && rm -f /dev/shm/KO8_4SU_labeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_4SU_labeled.unmutated.bam.flagstat
Submitted job 84 with external jobid '19834947'.
[Fri Jul 23 12:16:42 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_4SU_labeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_4SU_labeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_4SU_labeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_4SU_labeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.unmutated.bam.flagstat
jobid: 86
wildcards: sample=WT3_4SU_labeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_4SU_labeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_4SU_labeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_4SU_labeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/WT3_4SU_labeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_4SU_labeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_4SU_labeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_4SU_labeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/WT3_4SU_labeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_4SU_labeled.plus.bam -o /dev/shm/WT3_4SU_labeled.mutated.plus.bam --readids /dev/shm/WT3_4SU_labeled.plus.readids -o2 /dev/shm/WT3_4SU_labeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_4SU_labeled.minus.bam -o /dev/shm/WT3_4SU_labeled.mutated.minus.bam --readids /dev/shm/WT3_4SU_labeled.minus.readids -o2 /dev/shm/WT3_4SU_labeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/WT3_4SU_labeled.mutated.bam /dev/shm/WT3_4SU_labeled.mutated.plus.bam /dev/shm/WT3_4SU_labeled.mutated.minus.bam && rm -f /dev/shm/WT3_4SU_labeled.mutated.plus.bam /dev/shm/WT3_4SU_labeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.mutated.bam /dev/shm/WT3_4SU_labeled.mutated.bam && rm -f /dev/shm/WT3_4SU_labeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/WT3_4SU_labeled.unmutated.bam /dev/shm/WT3_4SU_labeled.unmutated.plus.bam /dev/shm/WT3_4SU_labeled.unmutated.minus.bam && rm -f /dev/shm/WT3_4SU_labeled.unmutated.plus.bam /dev/shm/WT3_4SU_labeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.unmutated.bam /dev/shm/WT3_4SU_labeled.unmutated.bam && rm -f /dev/shm/WT3_4SU_labeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_4SU_labeled.unmutated.bam.flagstat
Submitted job 86 with external jobid '19834950'.
[Fri Jul 23 12:16:48 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_4SU_labeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_4SU_labeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_4SU_labeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_4SU_labeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.unmutated.bam.flagstat
jobid: 88
wildcards: sample=WT4_4SU_labeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_4SU_labeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_4SU_labeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_4SU_labeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/WT4_4SU_labeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_4SU_labeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_4SU_labeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_4SU_labeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/WT4_4SU_labeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_4SU_labeled.plus.bam -o /dev/shm/WT4_4SU_labeled.mutated.plus.bam --readids /dev/shm/WT4_4SU_labeled.plus.readids -o2 /dev/shm/WT4_4SU_labeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_4SU_labeled.minus.bam -o /dev/shm/WT4_4SU_labeled.mutated.minus.bam --readids /dev/shm/WT4_4SU_labeled.minus.readids -o2 /dev/shm/WT4_4SU_labeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/WT4_4SU_labeled.mutated.bam /dev/shm/WT4_4SU_labeled.mutated.plus.bam /dev/shm/WT4_4SU_labeled.mutated.minus.bam && rm -f /dev/shm/WT4_4SU_labeled.mutated.plus.bam /dev/shm/WT4_4SU_labeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.mutated.bam /dev/shm/WT4_4SU_labeled.mutated.bam && rm -f /dev/shm/WT4_4SU_labeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/WT4_4SU_labeled.unmutated.bam /dev/shm/WT4_4SU_labeled.unmutated.plus.bam /dev/shm/WT4_4SU_labeled.unmutated.minus.bam && rm -f /dev/shm/WT4_4SU_labeled.unmutated.plus.bam /dev/shm/WT4_4SU_labeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.unmutated.bam /dev/shm/WT4_4SU_labeled.unmutated.bam && rm -f /dev/shm/WT4_4SU_labeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_4SU_labeled.unmutated.bam.flagstat
Submitted job 88 with external jobid '19834973'.
[Fri Jul 23 12:16:51 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam.flagstat
jobid: 90
wildcards: sample=SRA_labeled_1
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/SRA_labeled_1.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/SRA_labeled_1.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.plus.bam -o /dev/shm/SRA_labeled_1.mutated.plus.bam --readids /dev/shm/SRA_labeled_1.plus.readids -o2 /dev/shm/SRA_labeled_1.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.minus.bam -o /dev/shm/SRA_labeled_1.mutated.minus.bam --readids /dev/shm/SRA_labeled_1.minus.readids -o2 /dev/shm/SRA_labeled_1.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/SRA_labeled_1.mutated.bam /dev/shm/SRA_labeled_1.mutated.plus.bam /dev/shm/SRA_labeled_1.mutated.minus.bam && rm -f /dev/shm/SRA_labeled_1.mutated.plus.bam /dev/shm/SRA_labeled_1.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam /dev/shm/SRA_labeled_1.mutated.bam && rm -f /dev/shm/SRA_labeled_1.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/SRA_labeled_1.unmutated.bam /dev/shm/SRA_labeled_1.unmutated.plus.bam /dev/shm/SRA_labeled_1.unmutated.minus.bam && rm -f /dev/shm/SRA_labeled_1.unmutated.plus.bam /dev/shm/SRA_labeled_1.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam /dev/shm/SRA_labeled_1.unmutated.bam && rm -f /dev/shm/SRA_labeled_1.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam.flagstat
Submitted job 90 with external jobid '19834977'.
[Fri Jul 23 12:16:55 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam.flagstat
jobid: 92
wildcards: sample=SRA_unlabeled_1
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/SRA_unlabeled_1.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/SRA_unlabeled_1.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.plus.bam -o /dev/shm/SRA_unlabeled_1.mutated.plus.bam --readids /dev/shm/SRA_unlabeled_1.plus.readids -o2 /dev/shm/SRA_unlabeled_1.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.minus.bam -o /dev/shm/SRA_unlabeled_1.mutated.minus.bam --readids /dev/shm/SRA_unlabeled_1.minus.readids -o2 /dev/shm/SRA_unlabeled_1.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/SRA_unlabeled_1.mutated.bam /dev/shm/SRA_unlabeled_1.mutated.plus.bam /dev/shm/SRA_unlabeled_1.mutated.minus.bam && rm -f /dev/shm/SRA_unlabeled_1.mutated.plus.bam /dev/shm/SRA_unlabeled_1.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam /dev/shm/SRA_unlabeled_1.mutated.bam && rm -f /dev/shm/SRA_unlabeled_1.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/SRA_unlabeled_1.unmutated.bam /dev/shm/SRA_unlabeled_1.unmutated.plus.bam /dev/shm/SRA_unlabeled_1.unmutated.minus.bam && rm -f /dev/shm/SRA_unlabeled_1.unmutated.plus.bam /dev/shm/SRA_unlabeled_1.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam /dev/shm/SRA_unlabeled_1.unmutated.bam && rm -f /dev/shm/SRA_unlabeled_1.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam.flagstat
Submitted job 92 with external jobid '19834980'.
[Fri Jul 23 12:16:57 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep2_unlabeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep2_unlabeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep2_unlabeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep2_unlabeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.unmutated.bam.flagstat
jobid: 95
wildcards: sample=KO1_techrep2_unlabeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep2_unlabeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep2_unlabeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep2_unlabeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/KO1_techrep2_unlabeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep2_unlabeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_techrep2_unlabeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep2_unlabeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/KO1_techrep2_unlabeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep2_unlabeled.plus.bam -o /dev/shm/KO1_techrep2_unlabeled.mutated.plus.bam --readids /dev/shm/KO1_techrep2_unlabeled.plus.readids -o2 /dev/shm/KO1_techrep2_unlabeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_techrep2_unlabeled.minus.bam -o /dev/shm/KO1_techrep2_unlabeled.mutated.minus.bam --readids /dev/shm/KO1_techrep2_unlabeled.minus.readids -o2 /dev/shm/KO1_techrep2_unlabeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/KO1_techrep2_unlabeled.mutated.bam /dev/shm/KO1_techrep2_unlabeled.mutated.plus.bam /dev/shm/KO1_techrep2_unlabeled.mutated.minus.bam && rm -f /dev/shm/KO1_techrep2_unlabeled.mutated.plus.bam /dev/shm/KO1_techrep2_unlabeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.mutated.bam /dev/shm/KO1_techrep2_unlabeled.mutated.bam && rm -f /dev/shm/KO1_techrep2_unlabeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/KO1_techrep2_unlabeled.unmutated.bam /dev/shm/KO1_techrep2_unlabeled.unmutated.plus.bam /dev/shm/KO1_techrep2_unlabeled.unmutated.minus.bam && rm -f /dev/shm/KO1_techrep2_unlabeled.unmutated.plus.bam /dev/shm/KO1_techrep2_unlabeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.unmutated.bam /dev/shm/KO1_techrep2_unlabeled.unmutated.bam && rm -f /dev/shm/KO1_techrep2_unlabeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_techrep2_unlabeled.unmutated.bam.flagstat
Submitted job 95 with external jobid '19834985'.
[Fri Jul 23 12:16:58 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_unlabeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_unlabeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_unlabeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_unlabeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.unmutated.bam.flagstat
jobid: 83
wildcards: sample=KO1_unlabeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_unlabeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_unlabeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_unlabeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/KO1_unlabeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_unlabeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO1_unlabeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_unlabeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/KO1_unlabeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_unlabeled.plus.bam -o /dev/shm/KO1_unlabeled.mutated.plus.bam --readids /dev/shm/KO1_unlabeled.plus.readids -o2 /dev/shm/KO1_unlabeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO1_unlabeled.minus.bam -o /dev/shm/KO1_unlabeled.mutated.minus.bam --readids /dev/shm/KO1_unlabeled.minus.readids -o2 /dev/shm/KO1_unlabeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/KO1_unlabeled.mutated.bam /dev/shm/KO1_unlabeled.mutated.plus.bam /dev/shm/KO1_unlabeled.mutated.minus.bam && rm -f /dev/shm/KO1_unlabeled.mutated.plus.bam /dev/shm/KO1_unlabeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.mutated.bam /dev/shm/KO1_unlabeled.mutated.bam && rm -f /dev/shm/KO1_unlabeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/KO1_unlabeled.unmutated.bam /dev/shm/KO1_unlabeled.unmutated.plus.bam /dev/shm/KO1_unlabeled.unmutated.minus.bam && rm -f /dev/shm/KO1_unlabeled.unmutated.plus.bam /dev/shm/KO1_unlabeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.unmutated.bam /dev/shm/KO1_unlabeled.unmutated.bam && rm -f /dev/shm/KO1_unlabeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO1_unlabeled.unmutated.bam.flagstat
Submitted job 83 with external jobid '19834989'.
[Fri Jul 23 12:17:01 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_unlabeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_unlabeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_unlabeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_unlabeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.unmutated.bam.flagstat
jobid: 85
wildcards: sample=KO8_unlabeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_unlabeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_unlabeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_unlabeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/KO8_unlabeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_unlabeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/KO8_unlabeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_unlabeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/KO8_unlabeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_unlabeled.plus.bam -o /dev/shm/KO8_unlabeled.mutated.plus.bam --readids /dev/shm/KO8_unlabeled.plus.readids -o2 /dev/shm/KO8_unlabeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/KO8_unlabeled.minus.bam -o /dev/shm/KO8_unlabeled.mutated.minus.bam --readids /dev/shm/KO8_unlabeled.minus.readids -o2 /dev/shm/KO8_unlabeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/KO8_unlabeled.mutated.bam /dev/shm/KO8_unlabeled.mutated.plus.bam /dev/shm/KO8_unlabeled.mutated.minus.bam && rm -f /dev/shm/KO8_unlabeled.mutated.plus.bam /dev/shm/KO8_unlabeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.mutated.bam /dev/shm/KO8_unlabeled.mutated.bam && rm -f /dev/shm/KO8_unlabeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/KO8_unlabeled.unmutated.bam /dev/shm/KO8_unlabeled.unmutated.plus.bam /dev/shm/KO8_unlabeled.unmutated.minus.bam && rm -f /dev/shm/KO8_unlabeled.unmutated.plus.bam /dev/shm/KO8_unlabeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.unmutated.bam /dev/shm/KO8_unlabeled.unmutated.bam && rm -f /dev/shm/KO8_unlabeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/KO8_unlabeled.unmutated.bam.flagstat
Submitted job 85 with external jobid '19834993'.
[Fri Jul 23 12:17:02 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_unlabeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_unlabeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_unlabeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_unlabeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.unmutated.bam.flagstat
jobid: 87
wildcards: sample=WT3_unlabeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_unlabeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_unlabeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_unlabeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/WT3_unlabeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_unlabeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT3_unlabeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_unlabeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/WT3_unlabeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_unlabeled.plus.bam -o /dev/shm/WT3_unlabeled.mutated.plus.bam --readids /dev/shm/WT3_unlabeled.plus.readids -o2 /dev/shm/WT3_unlabeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT3_unlabeled.minus.bam -o /dev/shm/WT3_unlabeled.mutated.minus.bam --readids /dev/shm/WT3_unlabeled.minus.readids -o2 /dev/shm/WT3_unlabeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/WT3_unlabeled.mutated.bam /dev/shm/WT3_unlabeled.mutated.plus.bam /dev/shm/WT3_unlabeled.mutated.minus.bam && rm -f /dev/shm/WT3_unlabeled.mutated.plus.bam /dev/shm/WT3_unlabeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.mutated.bam /dev/shm/WT3_unlabeled.mutated.bam && rm -f /dev/shm/WT3_unlabeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/WT3_unlabeled.unmutated.bam /dev/shm/WT3_unlabeled.unmutated.plus.bam /dev/shm/WT3_unlabeled.unmutated.minus.bam && rm -f /dev/shm/WT3_unlabeled.unmutated.plus.bam /dev/shm/WT3_unlabeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.unmutated.bam /dev/shm/WT3_unlabeled.unmutated.bam && rm -f /dev/shm/WT3_unlabeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT3_unlabeled.unmutated.bam.flagstat
Submitted job 87 with external jobid '19834997'.
[Fri Jul 23 12:17:03 2021]
rule split_bam_by_mutation:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_unlabeled.plus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_unlabeled.minus.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_unlabeled.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_unlabeled.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.unmutated.bam.flagstat
jobid: 89
wildcards: sample=WT4_unlabeled
threads: 4
# using sam2tsv from jvarkit --> https://lindenb.github.io/jvarkit/Sam2Tsv.html
plusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_unlabeled.plus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_unlabeled.plus.vcf.gz > /dev/shm/${plusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_unlabeled.plus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${plusvcf%.*} "T" "C" | sort | uniq > /dev/shm/WT4_unlabeled.plus.readids
minusvcf=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_unlabeled.minus.vcf.gz)
zcat /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/WT4_unlabeled.minus.vcf.gz > /dev/shm/${minusvcf%.*}
java -Xmx200g -jar /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/sam2tsv.jar --reference /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.plus_rDNA_plus_5S.id90_masked.fa --skip-N /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_unlabeled.minus.bam | python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/tsv2readids.py /dev/shm/${minusvcf%.*} "A" "G" | sort | uniq > /dev/shm/WT4_unlabeled.minus.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_unlabeled.plus.bam -o /dev/shm/WT4_unlabeled.mutated.plus.bam --readids /dev/shm/WT4_unlabeled.plus.readids -o2 /dev/shm/WT4_unlabeled.unmutated.plus.bam
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_bam_by_readids.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/WT4_unlabeled.minus.bam -o /dev/shm/WT4_unlabeled.mutated.minus.bam --readids /dev/shm/WT4_unlabeled.minus.readids -o2 /dev/shm/WT4_unlabeled.unmutated.minus.bam
samtools merge -c -f -p -@ 4 /dev/shm/WT4_unlabeled.mutated.bam /dev/shm/WT4_unlabeled.mutated.plus.bam /dev/shm/WT4_unlabeled.mutated.minus.bam && rm -f /dev/shm/WT4_unlabeled.mutated.plus.bam /dev/shm/WT4_unlabeled.mutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.mutated.bam /dev/shm/WT4_unlabeled.mutated.bam && rm -f /dev/shm/WT4_unlabeled.mutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.mutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.mutated.bam.flagstat
samtools merge -c -f -p -@ 4 /dev/shm/WT4_unlabeled.unmutated.bam /dev/shm/WT4_unlabeled.unmutated.plus.bam /dev/shm/WT4_unlabeled.unmutated.minus.bam && rm -f /dev/shm/WT4_unlabeled.unmutated.plus.bam /dev/shm/WT4_unlabeled.unmutated.minus.bam
sambamba sort --memory-limit=200G --tmpdir=/dev/shm --nthreads=4 --out=/data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.unmutated.bam /dev/shm/WT4_unlabeled.unmutated.bam && rm -f /dev/shm/WT4_unlabeled.unmutated.bam
sambamba flagstat --nthreads=4 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.unmutated.bam > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/WT4_unlabeled.unmutated.bam.flagstat
Submitted job 89 with external jobid '19835000'.
[Fri Jul 23 12:29:38 2021]
Finished job 93.
1 of 82 steps (1%) done
[Fri Jul 23 12:29:38 2021]
localrule get_nfragments_json:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/raw_fastq/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/trim/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/fastuniq/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.post_secondary_supplementary_filter.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.post_insertion_filter.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.plus.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_2.minus.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_2.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/qc/nfragments/SRA_unlabeled_2.json
jobid: 190
wildcards: sample=SRA_unlabeled_2
cd /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/get_per_sample_nfragments.py SRA_unlabeled_2 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/qc/nfragments/SRA_unlabeled_2.json
[Fri Jul 23 12:29:38 2021]
rule get_split_reads:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_2.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_2.R2.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.mutated.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.mutated.R2.fastq.gz
jobid: 137
wildcards: sample=SRA_unlabeled_2, mutated=mutated
samtools view /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam|cut -f1|sort|uniq > /dev/shm/SRA_unlabeled_2.mutated.readids
R1fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.mutated.R1.fastq.gz)
R1fastq="/dev/shm/${R1fastq%.*}"
R2fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.mutated.R2.fastq.gz)
R2fastq="/dev/shm/${R2fastq%.*}"
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_2.R1.fastq.gz --outfq $R1fastq --readids /dev/shm/SRA_unlabeled_2.mutated.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_2.R2.fastq.gz --outfq $R2fastq --readids /dev/shm/SRA_unlabeled_2.mutated.readids
cd /dev/shm
/gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/fastq_pair $R1fastq $R2fastq
pigz -p4 ${R1fastq}.paired.fq
pigz -p4 ${R2fastq}.paired.fq
rsync -az --progress ${R1fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.mutated.R1.fastq.gz
rsync -az --progress ${R2fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.mutated.R2.fastq.gz
rm -rf /dev/shm/*.fastq /dev/shm/*.fq /dev/shm/*.fq.gz /dev/shm/*.fastq.gz /dev/shm/*.readids
[Fri Jul 23 12:29:39 2021]
Finished job 190.
2 of 82 steps (2%) done
Submitted job 137 with external jobid '19835993'.
[Fri Jul 23 12:29:44 2021]
rule htseq:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
jobid: 110
wildcards: sample=SRA_unlabeled_2
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_unlabeled_2.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_unlabeled_2.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
Submitted job 110 with external jobid '19835996'.
[Fri Jul 23 12:29:48 2021]
rule get_split_reads:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_2.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_2.R2.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.unmutated.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.unmutated.R2.fastq.gz
jobid: 138
wildcards: sample=SRA_unlabeled_2, mutated=unmutated
samtools view /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam|cut -f1|sort|uniq > /dev/shm/SRA_unlabeled_2.unmutated.readids
R1fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.unmutated.R1.fastq.gz)
R1fastq="/dev/shm/${R1fastq%.*}"
R2fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.unmutated.R2.fastq.gz)
R2fastq="/dev/shm/${R2fastq%.*}"
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_2.R1.fastq.gz --outfq $R1fastq --readids /dev/shm/SRA_unlabeled_2.unmutated.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_2.R2.fastq.gz --outfq $R2fastq --readids /dev/shm/SRA_unlabeled_2.unmutated.readids
cd /dev/shm
/gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/fastq_pair $R1fastq $R2fastq
pigz -p4 ${R1fastq}.paired.fq
pigz -p4 ${R2fastq}.paired.fq
rsync -az --progress ${R1fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.unmutated.R1.fastq.gz
rsync -az --progress ${R2fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_2.unmutated.R2.fastq.gz
rm -rf /dev/shm/*.fastq /dev/shm/*.fq /dev/shm/*.fq.gz /dev/shm/*.fastq.gz /dev/shm/*.readids
Submitted job 138 with external jobid '19835997'.
[Fri Jul 23 12:34:13 2021]
Finished job 90.
3 of 82 steps (4%) done
[Fri Jul 23 12:34:13 2021]
localrule get_nfragments_json:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/raw_fastq/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/trim/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/fastuniq/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.post_secondary_supplementary_filter.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.post_insertion_filter.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.plus.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_1.minus.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_1.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/qc/nfragments/SRA_labeled_1.json
jobid: 187
wildcards: sample=SRA_labeled_1
cd /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/get_per_sample_nfragments.py SRA_labeled_1 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/qc/nfragments/SRA_labeled_1.json
[Fri Jul 23 12:34:13 2021]
rule get_split_reads:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_1.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_1.R2.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.mutated.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.mutated.R2.fastq.gz
jobid: 131
wildcards: sample=SRA_labeled_1, mutated=mutated
samtools view /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam|cut -f1|sort|uniq > /dev/shm/SRA_labeled_1.mutated.readids
R1fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.mutated.R1.fastq.gz)
R1fastq="/dev/shm/${R1fastq%.*}"
R2fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.mutated.R2.fastq.gz)
R2fastq="/dev/shm/${R2fastq%.*}"
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_1.R1.fastq.gz --outfq $R1fastq --readids /dev/shm/SRA_labeled_1.mutated.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_1.R2.fastq.gz --outfq $R2fastq --readids /dev/shm/SRA_labeled_1.mutated.readids
cd /dev/shm
/gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/fastq_pair $R1fastq $R2fastq
pigz -p4 ${R1fastq}.paired.fq
pigz -p4 ${R2fastq}.paired.fq
rsync -az --progress ${R1fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.mutated.R1.fastq.gz
rsync -az --progress ${R2fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.mutated.R2.fastq.gz
rm -rf /dev/shm/*.fastq /dev/shm/*.fq /dev/shm/*.fq.gz /dev/shm/*.fastq.gz /dev/shm/*.readids
[Fri Jul 23 12:34:14 2021]
Finished job 187.
4 of 82 steps (5%) done
Submitted job 131 with external jobid '19836343'.
[Fri Jul 23 12:34:17 2021]
rule get_split_reads:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_1.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_1.R2.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.unmutated.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.unmutated.R2.fastq.gz
jobid: 132
wildcards: sample=SRA_labeled_1, mutated=unmutated
samtools view /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam|cut -f1|sort|uniq > /dev/shm/SRA_labeled_1.unmutated.readids
R1fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.unmutated.R1.fastq.gz)
R1fastq="/dev/shm/${R1fastq%.*}"
R2fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.unmutated.R2.fastq.gz)
R2fastq="/dev/shm/${R2fastq%.*}"
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_1.R1.fastq.gz --outfq $R1fastq --readids /dev/shm/SRA_labeled_1.unmutated.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_1.R2.fastq.gz --outfq $R2fastq --readids /dev/shm/SRA_labeled_1.unmutated.readids
cd /dev/shm
/gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/fastq_pair $R1fastq $R2fastq
pigz -p4 ${R1fastq}.paired.fq
pigz -p4 ${R2fastq}.paired.fq
rsync -az --progress ${R1fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.unmutated.R1.fastq.gz
rsync -az --progress ${R2fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_1.unmutated.R2.fastq.gz
rm -rf /dev/shm/*.fastq /dev/shm/*.fq /dev/shm/*.fq.gz /dev/shm/*.fastq.gz /dev/shm/*.readids
Submitted job 132 with external jobid '19836347'.
[Fri Jul 23 12:34:24 2021]
rule htseq:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.gene.counts
jobid: 107
wildcards: sample=SRA_labeled_1
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_labeled_1.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_labeled_1.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.gene.counts
Submitted job 107 with external jobid '19836352'.
[Fri Jul 23 12:34:48 2021]
Finished job 137.
5 of 82 steps (6%) done
[Fri Jul 23 12:35:00 2021]
Error in rule htseq:
jobid: 110
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
shell:
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_unlabeled_2.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_unlabeled_2.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 19835996
Error executing rule htseq on cluster (jobid: 110, external: 19835996, jobscript: /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/.snakemake/tmp.ckds4cod/snakejob.htseq.110.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 110.
[Fri Jul 23 12:35:00 2021]
rule htseq:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
jobid: 110
wildcards: sample=SRA_unlabeled_2
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_unlabeled_2.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_unlabeled_2.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
Submitted job 110 with external jobid '19836404'.
[Fri Jul 23 12:35:32 2021]
Finished job 92.
6 of 82 steps (7%) done
[Fri Jul 23 12:35:32 2021]
localrule get_nfragments_json:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/raw_fastq/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/trim/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/fastuniq/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.post_secondary_supplementary_filter.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.post_insertion_filter.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.plus.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_unlabeled_1.minus.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_unlabeled_1.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/qc/nfragments/SRA_unlabeled_1.json
jobid: 189
wildcards: sample=SRA_unlabeled_1
cd /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/get_per_sample_nfragments.py SRA_unlabeled_1 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/qc/nfragments/SRA_unlabeled_1.json
[Fri Jul 23 12:35:32 2021]
rule get_split_reads:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_1.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_1.R2.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.unmutated.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.unmutated.R2.fastq.gz
jobid: 136
wildcards: sample=SRA_unlabeled_1, mutated=unmutated
samtools view /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam|cut -f1|sort|uniq > /dev/shm/SRA_unlabeled_1.unmutated.readids
R1fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.unmutated.R1.fastq.gz)
R1fastq="/dev/shm/${R1fastq%.*}"
R2fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.unmutated.R2.fastq.gz)
R2fastq="/dev/shm/${R2fastq%.*}"
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_1.R1.fastq.gz --outfq $R1fastq --readids /dev/shm/SRA_unlabeled_1.unmutated.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_1.R2.fastq.gz --outfq $R2fastq --readids /dev/shm/SRA_unlabeled_1.unmutated.readids
cd /dev/shm
/gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/fastq_pair $R1fastq $R2fastq
pigz -p4 ${R1fastq}.paired.fq
pigz -p4 ${R2fastq}.paired.fq
rsync -az --progress ${R1fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.unmutated.R1.fastq.gz
rsync -az --progress ${R2fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.unmutated.R2.fastq.gz
rm -rf /dev/shm/*.fastq /dev/shm/*.fq /dev/shm/*.fq.gz /dev/shm/*.fastq.gz /dev/shm/*.readids
[Fri Jul 23 12:35:34 2021]
Finished job 189.
7 of 82 steps (9%) done
Submitted job 136 with external jobid '19836448'.
[Fri Jul 23 12:35:34 2021]
rule htseq:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.gene.counts
jobid: 109
wildcards: sample=SRA_unlabeled_1
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_unlabeled_1.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_unlabeled_1.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.gene.counts
Submitted job 109 with external jobid '19836451'.
[Fri Jul 23 12:35:35 2021]
rule get_split_reads:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_1.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_1.R2.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.mutated.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.mutated.R2.fastq.gz
jobid: 135
wildcards: sample=SRA_unlabeled_1, mutated=mutated
samtools view /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam|cut -f1|sort|uniq > /dev/shm/SRA_unlabeled_1.mutated.readids
R1fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.mutated.R1.fastq.gz)
R1fastq="/dev/shm/${R1fastq%.*}"
R2fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.mutated.R2.fastq.gz)
R2fastq="/dev/shm/${R2fastq%.*}"
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_1.R1.fastq.gz --outfq $R1fastq --readids /dev/shm/SRA_unlabeled_1.mutated.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_unlabeled_1.R2.fastq.gz --outfq $R2fastq --readids /dev/shm/SRA_unlabeled_1.mutated.readids
cd /dev/shm
/gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/fastq_pair $R1fastq $R2fastq
pigz -p4 ${R1fastq}.paired.fq
pigz -p4 ${R2fastq}.paired.fq
rsync -az --progress ${R1fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.mutated.R1.fastq.gz
rsync -az --progress ${R2fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_unlabeled_1.mutated.R2.fastq.gz
rm -rf /dev/shm/*.fastq /dev/shm/*.fq /dev/shm/*.fq.gz /dev/shm/*.fastq.gz /dev/shm/*.readids
Submitted job 135 with external jobid '19836453'.
[Fri Jul 23 12:37:33 2021]
Finished job 138.
8 of 82 steps (10%) done
[Fri Jul 23 12:37:45 2021]
Error in rule htseq:
jobid: 107
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.gene.counts
shell:
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_labeled_1.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_labeled_1.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.gene.counts
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 19836352
Error executing rule htseq on cluster (jobid: 107, external: 19836352, jobscript: /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/.snakemake/tmp.ckds4cod/snakejob.htseq.107.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 107.
[Fri Jul 23 12:37:45 2021]
Error in rule htseq:
jobid: 110
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
shell:
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_unlabeled_2.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_unlabeled_2.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 19836404
Error executing rule htseq on cluster (jobid: 110, external: 19836404, jobscript: /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/.snakemake/tmp.ckds4cod/snakejob.htseq.110.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 110.
[Fri Jul 23 12:37:45 2021]
rule htseq:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.gene.counts
jobid: 107
wildcards: sample=SRA_labeled_1
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_labeled_1.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_labeled_1.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_1.unmutated.gene.counts
Submitted job 107 with external jobid '19836628'.
[Fri Jul 23 12:37:49 2021]
rule htseq:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
jobid: 110
wildcards: sample=SRA_unlabeled_2
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_unlabeled_2.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_unlabeled_2.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_2.unmutated.gene.counts
Submitted job 110 with external jobid '19836632'.
[Fri Jul 23 12:37:57 2021]
Error in rule htseq:
jobid: 109
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.gene.counts
shell:
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_unlabeled_1.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_unlabeled_1.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.gene.counts
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 19836451
Error executing rule htseq on cluster (jobid: 109, external: 19836451, jobscript: /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/.snakemake/tmp.ckds4cod/snakejob.htseq.109.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 109.
[Fri Jul 23 12:37:57 2021]
rule htseq:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.gene.counts
jobid: 109
wildcards: sample=SRA_unlabeled_1
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_unlabeled_1.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_unlabeled_1.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_unlabeled_1.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_unlabeled_1.unmutated.gene.counts
Submitted job 109 with external jobid '19836642'.
[Fri Jul 23 12:39:57 2021]
Finished job 131.
9 of 82 steps (11%) done
[Fri Jul 23 12:40:20 2021]
Finished job 135.
10 of 82 steps (12%) done
[Fri Jul 23 12:41:14 2021]
Finished job 91.
11 of 82 steps (13%) done
[Fri Jul 23 12:41:14 2021]
localrule get_nfragments_json:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/raw_fastq/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/trim/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/fastuniq/lanes.txt, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.post_secondary_supplementary_filter.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.post_insertion_filter.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.plus.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/hisat2/SRA_labeled_2.minus.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam.flagstat, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.plus.vcf.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/vcf/SRA_labeled_2.minus.vcf.gz
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/qc/nfragments/SRA_labeled_2.json
jobid: 188
wildcards: sample=SRA_labeled_2
cd /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/get_per_sample_nfragments.py SRA_labeled_2 /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/qc/nfragments/SRA_labeled_2.json
[Fri Jul 23 12:41:14 2021]
rule htseq:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_2.mutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_2.mutated.gene.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_2.unmutated.exon.counts, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_2.unmutated.gene.counts
jobid: 108
wildcards: sample=SRA_labeled_2
infer_experiment.py -i /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam -r /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/mm10.bed12 -s 500000 > /dev/shm/SRA_labeled_2.strand.info
strandedness=$(tail -n1 /dev/shm/SRA_labeled_2.strand.info|awk '{if ( $NF > 0.75 ) {print "reverse"} else if ( $NF < 0.25 ) {print "yes"} else {print "no"}}')
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_2.mutated.exon.counts
htseq-count -t "exon" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_2.unmutated.exon.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_2.mutated.gene.counts
htseq-count -t "gene" -f bam -r pos --stranded $strandedness --mode intersection-nonempty --additional-attr=gene_name -f bam -r pos --stranded yes --additional-attr=gene_name /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam /data/RBL_NCI/Wolin/mESC_slam_analysis/resources/mm10/mm10.v25.plus_rDNA.plus_5S.gtf > /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/htseq/SRA_labeled_2.unmutated.gene.counts
[Fri Jul 23 12:41:15 2021]
Finished job 188.
12 of 82 steps (15%) done
Submitted job 108 with external jobid '19837228'.
[Fri Jul 23 12:41:16 2021]
rule get_split_reads:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_2.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_2.R2.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam
output: /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_2.mutated.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_2.mutated.R2.fastq.gz
jobid: 133
wildcards: sample=SRA_labeled_2, mutated=mutated
samtools view /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.mutated.bam|cut -f1|sort|uniq > /dev/shm/SRA_labeled_2.mutated.readids
R1fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_2.mutated.R1.fastq.gz)
R1fastq="/dev/shm/${R1fastq%.*}"
R2fastq=$(basename /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_2.mutated.R2.fastq.gz)
R2fastq="/dev/shm/${R2fastq%.*}"
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_2.R1.fastq.gz --outfq $R1fastq --readids /dev/shm/SRA_labeled_2.mutated.readids
python /gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/workflow/scripts/filter_fastq_by_readids_highmem.py --infq /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_2.R2.fastq.gz --outfq $R2fastq --readids /dev/shm/SRA_labeled_2.mutated.readids
cd /dev/shm
/gpfs/gsfs11/users/RBL_NCI/Wolin/mESC_slam_analysis/workflow/4SUseq/resources/fastq_pair $R1fastq $R2fastq
pigz -p4 ${R1fastq}.paired.fq
pigz -p4 ${R2fastq}.paired.fq
rsync -az --progress ${R1fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_2.mutated.R1.fastq.gz
rsync -az --progress ${R2fastq}.paired.fq.gz /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/filtered_reads/SRA_labeled_2.mutated.R2.fastq.gz
rm -rf /dev/shm/*.fastq /dev/shm/*.fq /dev/shm/*.fq.gz /dev/shm/*.fastq.gz /dev/shm/*.readids
Submitted job 133 with external jobid '19837230'.
[Fri Jul 23 12:41:19 2021]
rule get_split_reads:
input: /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_2.R1.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/fastqs/SRA_labeled_2.R2.fastq.gz, /data/RBL_NCI/Wolin/mESC_slam_analysis/find_mutations_072221/bams/SRA_labeled_2.unmutated.bam