Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

GATK Staff

Why does this work on command line but not when executed via cromwell?

I have the following commands wrapped in a WDL task:

        source /broad/software/scripts/useuse
        use BWA
        use Samtools
        bwa mem -t 8 -R ${read_group} ${ref} ${fq1} ${fq2} | samtools view -bS - > ${sample_name}.aligned.bam

The above is trying to generate an aligned BAM without the hard-disk overhead of an intermediary SAM file. It works when I do it manually on command line. However, when executed as part of a WDL, I get a truncated BAM that's only 93 bytes in size.The stderr doesn't show anything informative except I noticed that BWA reports a shorter CPU time than when I do it manually, which makes sense.

Any clue as to what might be happening or alternate ways to do this?



  • mcovarrmcovarr Cambridge, MAMember, Broadie, Dev

    Could you peek inside the appropriate script file in the job's execution directory to see if the bwa command that was written looks like what you expect?

Sign In or Register to comment.