too many memory and file handle resource required by GenotypeGVCFs

wang_yugui2wang_yugui2 china,beijingMember

Hi.

It seems that too many memory and file handle resource required by GenotypeGVCFs

command line:
java -XX:-UseCompressedOops -Xms1440g -XX:MinHeapFreeRatio=25 -XX:MaxHeapFreeRatio=50 -jar /usr/hpc-bio/gatk/GATK.jar -T GenotypeGVCFs -nt 120 -l WARN -R /usr/bio-ref/GRCh38.p9/GRCh38.dna.fa --dbsnp /usr/bio-ref/GRCh38.p9/dbsnp.vcf -nda -maxAltAlleles 25 -A AS_FisherStrand -A AS_QualByDepth -o /ssd//biowrk/CLP/vcf.gatk/proj.GenotypeGVCFs.vcf -V /ssd//biowrk/CLP/gvcf.gatk/1510100/hc.normal.g.vcf -V /ssd//biowrk/CLP/gvcf.gatk/1510109/hc.normal.g.vcf -V /ssd//biowrk/CLP/gvcf.gatk/1510110/hc.normal.g.vcf -V /ssd//biowrk/CLP/gvcf.gatk/1510111/hc.normal.g.vcf ...

g.vcf input: 95 exome
GenotypeGVCFs version:3.6 or 3.7 nightly( 3.7.0 with -nt is NG)
os:CentOS 7.3 (Linux R930 3.10.0-514.6.1.el7.x86_64) and other centos 7
java:1.8.0_121-b13 or 1.8.0_111 or others.

memory(RES): 0.840t -> too many memory is used? and it is always increasing when running.

file handle:

lsof -p 7724 |wc

11704 ; too many handles?

lsof -p 7724 |grep S15212|wc

120 ; a file is opened 120 times, can we open it only only?

Answers

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