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)