The current GATK version is 3.2-2

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

# Is the parallelism documentation for DepthOfCoverage correct?

Jamaica Plain, MAPosts: 6Member, Broadie, Cancer Tools Developer

Parallelism options

This tool can be run in multi-threaded mode using this option.

TreeReducible (-nt)

Yet when I run the GATK with -nt, I get an error that -nt is not supported (truncated to save space):

ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a): ERROR MESSAGE: Invalid command line: Argument nt has a bad value: The analysis DepthOfCoverage aggregates results by interval. Due to a current limitation of the GATK, analyses of this type do not currently support parallel execution. Please run your analysis without the -nt option.

Tagged:

• Jamaica Plain, MAPosts: 6Member, Broadie, Cancer Tools Developer

Apologies for the poor markdown

No worries. We'll improve the error message on this for the next version; the issue is that by default, the tool produces a summary of data aggregated over intervals, which is not compatible with multithreading. However, if you disable the per-interval reporting (see -omitIntervalStatistics ifI remember correctly), you will be able to use the multithreading.

Geraldine Van der Auwera, PhD

• Jamaica Plain, MAPosts: 6Member, Broadie, Cancer Tools Developer

--omitIntervalStatistics got rid of the error. Thanks!

• Posts: 17Member
edited January 14

So, what is the max memory that could be allocated to depthOfCoverage I use -Xmx2G.....I use the older GATK version GenomeAnalysisTK-1.6-13, hence cannot use multithreading option, i,.e -nt But if I go more that 2G on the -Xmx value then I think it wont make any difference..correct?

Post edited by Shrey_S on

Hi @Shrey_S,

I would say that's correct, yes -- I wouldn't expect memory to be the limiting factor for DepthOfCoverage, so increasing the allocation won't make it go faster, unfortunately.

Geraldine Van der Auwera, PhD

• Posts: 17Member

So that means if I use -Xmx6G it would still use 2G which is the max it could use... Is 2G the standard max memory for all the GATK tools (i.e. if we run them without multithreading)?