bcftools mpileup error

Question

[kat.bi]

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.

[Pierre Lindenbaum]

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'

[kat.bi]

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

[Pierre Lindenbaum]

The quote is required