Test-drive the GATK tools and Best Practices pipelines on Terra
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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.