Bioinformatics Asked by Vitaly on July 15, 2021
I am trying to establish pipeline in snakePipes and while running DNA mapping I got next IndexError error.
(snakePipes) ~ $ DNA-mapping -i /Volumes/HD2/snakePipes_CHIP/ChiPseq -o /Volumes/HD2/snakePipes_CHIP/ChiPseq1 --mapq 5 -j 10 --dedup hg38
Building DAG of jobs...
Using shell: /bin/bash
Provided cluster nodes: 10
Job counts:
count jobs
5 Bowtie2
5 FASTQ1
5 FASTQ2
rule origFASTQ2:
input: /Volumes/HD2/snakePipes_CHIP/ChiPseq/SRR6761499_R2.fastq.gz
output: originalFASTQ/SRR6761499_R2.fastq.gz
jobid: 75
wildcards: sample=SRR6761499
RuleException in line 9 of /Users/v/miniconda3/envs/snakePipes/lib/python3.6/site-packages/snakePipes/shared/rules/FASTQ.snakefile:
IndexError: list index out of range
Error: snakemake returned an error code of 1, so processing is incomplete!
When I am looking in FASTQ.snakefile:
rule origFASTQ1:
input:
indir+"/{sample}"+reads[0]+ext
output:
"originalFASTQ/{sample}"+reads[0]+".fastq.gz"
shell:
"( [ -f {output} ] || ln -s -r {input} {output} )"
line9: rule origFASTQ2:
input:
indir+"/{sample}"+reads[1]+ext
output:
"originalFASTQ/{sample}"+reads[1]+".fastq.gz"
shell:
"( [ -f {output} ] || ln -s -r {input} {output} )"
I do not understand why I see this error. I hope somebody can point me on the source of the error.
When I use –local parameter I do not see this error, however I get another error:
ln: illegal option -- r
usage: ln [-Ffhinsv] source_file [target_file]
ln [-Ffhinsv] source_file ... target_dir
link source_file target_file
output: originalFASTQ/SRR6761495_R1.fastq.gz
shell:
( [ -f originalFASTQ/SRR6761495_R1.fastq.gz ] || ln -s -r /Volumes/HD2/snakePipes_CHIP/ChiPseq/SRR6761495_R1.fastq.gz originalFASTQ/SRR6761495_R1.fastq.gz )
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
as far as I understand -r option creates symbolic links relative to link location
in /Volumes/HD2/snakePipes_CHIP/ChiPseq
I have:
Bowtie2 SRR6761495_R1.fastq.gz SRR6761495_R2.fastq.gz
command.sh SRR6761499_R1.fastq.gz SRR6761499_R2.fastq.gz
ChIPdict.yaml SRR6761497_R1.fastq.gz SRR6761497_R2.fastq.gz
deepTools_qc SRR6761498_R1.fastq.gz SRR6761498_R2.fastq.gz
fetch.sh SRR6761502_R1.fastq.gz SRR6761502_R2.fastq.gz
filtered_bam
Sambamba
rename_files.sh
I am working on macOS Catalina in bash shell and ln -r is valid option (I installed coreutils)
Thanks
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