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

Java & GATK using too many cores for calculating Depth of Coverage


I am running GATK 2.7.2 with Java 1.7 to calculate the Depth of Coverage using the command -

java -Xmx6100m -XX:ParallelGCThreads=1 -jar /projects/GenomeAnalysisTK-2.7-4-g6f46d11//GenomeAnalysisTK.jar -nct 1 -nt 1 -T DepthOfCoverage -I /scratch/AID1234.Improved.bam -L /projects/nimblv2.EXOME.interval_list -R /projects/fasta/Human_GRC_build37_1kGproject/human_g1k_v37_Ensembl_MT_66.fasta -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o /scratch/AID1234.txt

But when I check the details of the job with top command, I can see that a total of 10 cores are being used instead of 1.

Can someone tell me what I am doing wrong and how to overcome the problem.




Sign In or Register to comment.