To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Runtime Performance of UnifiedGenotyper slows down with increasing Thread size?

Hello there,

I have run GATK's UnifiedGenotyper tool with different thread sizes (9, 18, 36 on a 40-core machine) in order to see how well it scales for an increasing thread size. I first tried out UnifiedGenotyper of version 1.7 and set -nt to 9, 18, and 36 with 8GB heap assigned for a 88GB large BAM file, respectively.
When looking at the results, I noticed that runtime performance increased when using more threads, so I updated GATK to version 2.7-4 in order to check if this behavior has vanished with the newer version.
I also noticed then that there exists another thread-parameter for the number of cpu threads.

So, I ran GATK's UnifiedGenotyper version 2.7-4 for a 88GB large file on a 40-core linux machine with -nt 1, -nct 9/18/36, and assigned 8GB heap.
The behavior in runtime performance remained the same. What am I missing here?

Best,

Cindy

Best Answer

Answers

Sign In or Register to comment.