using parallel on samtools view
I cannot get this to work. > seems to be the problem. but I can't figure out how to fix it.
bam=bam_paths.txt
id=samples_ids.txt
parallel --xapply -j 5 'samtools view -b -f 4 {1} ">" ${outdir}/{2}.unmapped.bam' :::: $bam :::: $id
Error:
[W::sam_read1] Parse error at line 1
Failed to open BAM file LP60088.unmapped.bam
I have also tried:
parallel --xapply -j 5 samtools view -b -f 4 {1} ">" ${outdir}/{2}.unmapped.bam :::: $bam :::: $id
and
parallel --xapply -j 5 'samtools view -b -f 4 {1} |tee ${outdir}/{2}.unmapped.bam' :::: $bam :::: $id
All these gave me the same error. Can someone help please?
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michael.ante
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chictu •
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chictu •
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what is the output of
a list of paths to the bam files.
/working/sample/aligned_read_group/q/3e3d3282xxxx.bam /working/sample/aligned_read_group/d/f8dj39dd3xxxx.bam
...etc
and the id.txt is a list of sample names.
D01
D02
...etc
ok so that was not an error in your apths.txt file.
And
LP60088.unmapped.bamis a valid bam file from your input list having at least one read?LP60088.unmapped.bamis an outputWhich causes the error. Either you try to read that file despite the fact it isn't there or you don't have the permissions to write the file at the given location.
Have you tried using
samtoolsoutput option-oinstead of>?Yes I have. got the same error.