Why is BaseRecalibrator so slow - not using all threads?
Posted in Ask the team | Last updated on


Comments (4)

Hi,

I'm running BaseRecalibrator on a full lane of HiSeq. I set the -nct switch to 8, but I see that the average load is <1. Why is this so? Doesn't the BaseRecalibrator use threads properly?

I've seen this thread http://gatkforums.broadinstitute.org/discussion/1263/baserecalibrator-trade-off-between-runtime-and-accuracy on how to speed up the process by downsampling. Is this a better option considering I have >200M reads?

BTW I'm using version 2.2-8 - do newer versions implement -num_threads?

I would really love to reduce the runtime from 36hrs.

Many thanks.


Return to top Comment on this article in the forum