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GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

United KingdomMember Posts: 404 ✭✭✭

Does the walker DepthOfCoverage support multi-threading?

According to the documentation:
"This tool can be run in multi-threaded mode using this option. TreeReducible (-nt)"

When I try with GATK2.5 I get this 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."

Would it work, if I upgraded to 2.7? You upgrade GATK more frequently than I change my under wear, so it is difficult to keep up Thanks!

Tagged:

Hi Tommy,

If you don't mind I'll refrain from commenting on your personal hygiene and sartorial habits

But as regards to the issue you're running into: it's not really a version problem. What's happening here is that by default the DoC is set to generate stats averaged over intervals, which is not compatible with multithreading mode. If you pass the --omitIntervalStatistics / -omitIntervals flag this will be disabled and multithreading ability will be restored. We'll look at documenting and/or putting in a workaround to avoid this situation in the future.

Geraldine Van der Auwera, PhD

Hi Tommy,

If you don't mind I'll refrain from commenting on your personal hygiene and sartorial habits

But as regards to the issue you're running into: it's not really a version problem. What's happening here is that by default the DoC is set to generate stats averaged over intervals, which is not compatible with multithreading mode. If you pass the --omitIntervalStatistics / -omitIntervals` flag this will be disabled and multithreading ability will be restored. We'll look at documenting and/or putting in a workaround to avoid this situation in the future.

Geraldine Van der Auwera, PhD

• United KingdomMember Posts: 404 ✭✭✭

Thank you! I actually prefer getting an error message instead of occupying multiple processors for a single core job.