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# Why is BaseRecalibrator so slow - not using all threads?

Member

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?

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

Many thanks.

Tagged:

• Member

After a bit of investigating of parameters I've used the -dfrac 0.05 and -dt ALL_READS options to get my runtime down to ~3hrs.

However, the low amount of CPU load is still a concern.

You should definitely use the latest version to take advantage of recent improvements that have been made at many levels of the GATK -- such as the revamped downsampling engine which is less biased than the previous implementation.

BaseRecalibrator does not support the use of data threads (-nt), only cpu threads (-nct) which you're already using. I can't say why you would see a smaller cpu load than expected; the tool itself uses cpu threads just fine in our hands. Some people have platform or filesystem-related issues getting multithreading to work properly, but that's not something we can do anything about at the moment.