Open von1laughing opened 2 years ago
@von1laughing Can you try running jstack
on the running GATK process when the CPU usage is ~2400%, and paste the output here? This will produce a dump of the Java threads. You'll need to provide jstack with the process ID (pid) of the running Java process.
Bug Report
Affected tool(s) or class(es)
Affected version(s)
Description
I produced the bam files using STAR, and adjusted the MQ value to 60. I then used sambamba markdup to mark duplicate, then I proceeded to use SplitNCigarReads.
The CPU load for SplitNCigarReads was very high and at certain times can spike up to 2400%. I tried limiting the cpu usage with commands like
-XX:ParallelGCThreads=1
and-XX:ConcGCThreads=1
, but it doesn't seem to have an effect. (The cpu usage sometimes do stay at 100%) I also adjusted the MQ value in STAR to lessen the load in SplitNCigarReads. I also tried to increase the read size to reduce I/O time.Steps to reproduce
STAR
Mark Duplicate
SplitNCigarReads