This is a test version of Biostars. For the public version, visit https://www.biostars.org.
bcftools mpileup error

Hi, I'm trying to submit a variant calling job using bcftools mpileup into the HPC server like:

bsub -q prod -P gfap-anno-test -J gfap-anno-test -R "rusage[mem=9000,scr=5000] span[hosts=1]" -n 5 bcftools mpileup -Ou -f sample_dedupl.bam | bcftools call -mv -Ob -o out_sample.bcf

It throws an error - Failed to read from standard input: unknown file type

But when I executed this command in CLI itself for one sample, it started processing without any error.

Please suggest the solution or the issue associated with it.

bcftools variant-calling wgs
• 1,007 views • link
written by kat.bi • kat.bi

I don't know bsub but i would single-quote all the string 'bcftools mpileup -Ou -f sample_dedupl.bam | bcftools call -mv -Ob -o out_sample.bcf'

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

You meant the quote is required or the part with quote you posted alone will work?

• 0 views • link
written by kat.bi • kat.bi

0 answers

No answers yet.

Log in to answer this question.

More posts like this