CombineGVCF killed

lizhichao

Hi:
I try to place the gatk4 in docker image,then it always kills.But,when I set JVM:500M ,it's ok ,why? and I suppose it is slower running in 500M than default.
my command:
gatk=/opt/bin/gatk-4.0.3.
chr=chr1
fasta=/l3bioinfo/test-data/ucsc.hg19.fasta
$gatk --java-options -Xmx500m CombineGVCFs -R ${fasta} --variant /l3bioinfo/test-data/NA12878_chr1.HC.chr1.g.vcf.gz \
--variant /l3bioinfo/test-data/NA12878.HC.chr1.g.vcf.gz \
-O ${chr}.HC.g.vcf

Killed Image:

shlee

Hi @lizhichao, if you need more details on how to install GATK in your personal Docker, then please check out the READMEs at

• https://github.com/broadinstitute/gatk
• https://github.com/broadinstitute/gatk/tree/master/scripts/docker

and check out the scripts at

• https://github.com/broadinstitute/gatk/tree/master/scripts/docker/gatkbase

Good luck!

SkyWarrior

Why don't you use the official docker image for gatk ?

shlee

Hi @lizhichao,

You can find information on official resources on our Download page. Our Docker images are hosted on Dockerhub at https://hub.docker.com/r/broadinstitute/gatk.

lizhichao

First of all, thank you very much.
Because I try to package the tool and exposure parameters in order to can be seted according to the object required.

shlee

Hi @lizhichao, if you need more details on how to install GATK in your personal Docker, then please check out the READMEs at

• https://github.com/broadinstitute/gatk
• https://github.com/broadinstitute/gatk/tree/master/scripts/docker

and check out the scripts at

• https://github.com/broadinstitute/gatk/tree/master/scripts/docker/gatkbase

Good luck!

lizhichao

OK. Thanks very much for your help!