Question: Java memory issue in GATK
1
gravatar for boymin2020
2.1 years ago by
boymin202020
boymin202020 wrote:

I am using HaplotypeCaller of GATK to do variants calling for near 349 WGS human data, which means there are 349 jobs in the cluster. The following is my command.

java -Xmx4G \
-Djavaio.tmpdir=$tmp \
-jar $jar \
-T HaplotypeCaller \
-R $ref \
--genotyping_mode DISCOVERY \
-stand_call_conf 10 \
--emitRefConfidence GVCF \
--variant_index_type LINEAR \
--variant_index_parameter 128000 \
-D $DBSNP \
--comp:HapMapV3 $HpMpV3 \
-pairHMM VECTOR_LOGLESS_CACHING \
$infofields \
-log $log \
-I $bamFil \
-o $outVcf

An error came out for one job. It seems the cluster is short of memory. But I checked the memory usage, there was still many memory unused. Why it can not allocate memory to this job ?

Blockquote Java HotSpot(TM) 64-Bit Server VM warning: INFO: os::commit_memory(0x00000007b5080000, 168820736, 0) failed; error='Cannot allocate memory' (errno=12)

java gatk haplotypecaller • 1.2k views
ADD COMMENTlink modified 2.1 years ago by genomax65k • written 2.1 years ago by boymin202020
1

Did the specific node had more memory or the cluster in general? If the jobs are not distributed well enough, several jobs find themselves on the same node, exhausting its memory.

ADD REPLYlink written 2.1 years ago by Asaf5.5k

That is one kind of situation. But the job had run a long time and all of the nodes show very enough unused memory.

ADD REPLYlink written 2.1 years ago by boymin202020
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