I'm watching a job go through, and BWA finished a while ago, but the Samtools sort process is still running. We're only giving it a single core, I think this is because we use an older version? Christoph has done some work to show the best combination of cores for BWA piped to Samtools, so maybe he has some input.
I'm watching a job go through, and BWA finished a while ago, but the Samtools sort process is still running. We're only giving it a single core, I think this is because we use an older version? Christoph has done some work to show the best combination of cores for BWA piped to Samtools, so maybe he has some input.
https://github.com/tgen/pegasusPipe/blob/master/jobScripts/pegasus_bwaMem.pbs