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About CombineGVCFs

Hi,

I have about 600 g.vcf files after GATK haplotypecalling.
Then I want to combine the 600 g.vcf files.
I tried to combine 600 g.vcf files with GATK CombineGVCFs but I couldn't.
The command I used is as below.
----------
java -jar /home/h1kimura/lib/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar CombineGVCFs
-R /oasis/projects/nsf/ddp195/h1kimura/resources/human_g1k_v37_decoy.fasta
-V /oasis/projects/nsf/ddp195/h1kimura/exon_vcfs//gVCF.list
-O /oasis/projects/nsf/ddp195/h1kimura/exon_vcfs/combined_genotyped.vcf

gVCF.list includes 600 g.vcf files
----------------------
the erro message are as below
----------------------
07:30:27.308 INFO FeatureManager - Using codec VCFCodec to read file file:///oasis/projects/nsf/ddp195/h1kimura/exon_vcfs/NP070.raw_variants.g.vcf
07:30:41.618 INFO FeatureManager - Using codec VCFCodec to read file file:///oasis/projects/nsf/ddp195/h1kimura/exon_vcfs/NP071.raw_variants.g.vcf
08:29:17.988 INFO CombineGVCFs - Shutting down engine
[July 15, 2019 8:29:18 AM PDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 62.33 minutes.
Runtime.totalMemory()=26742882304
java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:202)
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:178)
at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:163)
at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:228)
at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:263)
at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(FeatureManager.java:234)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$initializeDrivingVariants$0(MultiVariantWalker.java:73)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.initializeDrivingVariants(MultiVariantWalker.java:63)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:55)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:697)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.onStartup(MultiVariantWalker.java:46)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:195)
... 18 more
Caused by: java.lang.OutOfMemoryError: Java heap space
at htsjdk.tribble.index.linear.LinearIndex$ChrIndex.read(LinearIndex.java:295)
at htsjdk.tribble.index.AbstractIndex.read(AbstractIndex.java:404)
at htsjdk.tribble.index.linear.LinearIndex.<init>(LinearIndex.java:116)
at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:195)
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:178)
at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:163)
at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:228)
at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:263)
at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(FeatureManager.java:234)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$initializeDrivingVariants$0(MultiVariantWalker.java:73)
at org.broadinstitute.hellbender.engine.MultiVariantWalker$$Lambda$69/1189187821.accept(Unknown Source)
... 12 more
---------------------
Could you tell me the how to combine the 600 g.vcf files?
Have I use the more cpus?

Thanks in advance.

Meganejin
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