Hello,

I'm using GATK version 4.1.0.0. I have 14 germline samples which I used to make a panel of normals. When running Mutect2 using my tumor WES samples and my panel of normals I get this memory error. I tried increasing the amount of RAM I was allocating, up to 200G, but this made no difference. I did try running this command with the Broad's panel of normals, 1000g_pon.hg38.vcf.gz, and it ran without any problems. How can I fix this error?

for file in /projects/b1042/MeeksLab/wes/new/trim/JMT1-2_*recal.bam

do

        java -jar /hpc/software/gatk/4.1.0/gatk-package-4.1.0.0-local.jar Mutect2 -R /projects/b1042/MeeksLab/knownsites/Homo_sapiens_assembly38.fasta -I $file --germline-resource /projects/b1042/MeeksLab/knownsites/af-only-gnomad.hg38.vcf.gz --panel-of-normals /projects/b1042/MeeksLab/19127-16_T1/trim/section.pon.vcf.gz -O ${file}.section.vcf.gz

done

Error:

/var/spool/slurmd/job3434781/slurm_script: line 11: 20164 Killed                  java -jar /hpc/software/gatk/4.1.0/gatk-package-4.1.0.0-local.jar Mutect2 -R /projects/b1042/MeeksLab/knownsites/Homo_sapiens_assembly38.fasta -I $file --germline-resource /projects/b1042/MeeksLab/knownsites/af-only-gnomad.hg38.vcf.gz --panel-of-normals /projects/b1042/MeeksLab/19127-16_T1/trim/section.pon.vcf.gz -O ${file}.section.vcf.gz

slurmstepd: error: Detected 1 oom-kill event(s) in step 3434781.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.