Hi,

I was running joint call for ~300 samples. GATK get an "OutOfMemoryError" when close to 95% completion, but the VCF was "successfully" produced and indexed.

If i did not manually examine the error log i would think it completed successfully.

In such cases, I think GATK should not generate the index file so we would know something went wrong (as the VCF would missing index file)?

Thank you

Shuoguo

=== details ===

Can you please provide
a) GATK version used

gatk-4.1.5.0

b) Exact GATK commands used

/gatk-4.1.5.0/gatk --java-options -Xmx12g HaplotypeCaller -R ref_genome.fa -I bam.245.list -O joint.chr9.vcf.gz --alleles chr9.vcf.gz -L chr9.list --interval-padding 50 --max-reads-per-alignment-start 0

c) The entire error log if applicable.

Runtime.totalMemory()=4114612224
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner.align(SmithWatermanJavaAligner.java:90)
at org.broadinstitute.hellbender.utils.read.AlignmentUtils.createReadAlignedToRef(AlignmentUtils.java:80)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils.realignReadsToTheirBestHaplotype(AssemblyBasedCallerUtils.java:84)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:599)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:212)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)