GATK creating hs_err_pid.log file

Question

[cvu]

Hi,

I am using GATK for variant calling, most of the time its working correctly for all steps, but some times its creating hs_err_pid***.log and then not completing that process and exiting.

Thanks

[iraun]

This error indicates a java VM crashing. I guess that there is some kind of problem related to java mem or threads, but I'm not a java expert. I think that it's nothing to worry about. Can you write the GATK command line you have used?

[cvu]

Below parameters I am using for GATK

java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R GRch38_p1_new.fasta -I realigned.bam -rf BadCigar -knownSites dbsnp_built142.vcf -o output.table

Answer 1

[Len Trigg]

The hs_err_pid.log files are indeed when the JVM crashes. Sometimes these are cases where there is a legitimate JVM bug, but more often it is due to the outer operating system killing the JVM, e.g:

• If your application is using more memory than the operating system can supply -- this can most commonly occur if you give -Xmx parameters that are too large for what can run on the machine for the duration of the run (for example if there are other memory intensive jobs running on the machine)
• If your application is running native code and that code contains bugs that cause segfault.

Look at the contents of the log files, and if you see messages referring to "insufficient memory" then you have the first case, and stand a chance of doing something about it by changing the memory allocation, reducing other jobs on the machine, etc :-)