Hi,
I am aware that some people have faced this error, but they are from old version of GATK and I am not sure if it applies to the GATK version I am using or not (4.0.1.2 with Java 1.8.0_74)..but I am facing these errors:
java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:190)
at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:162)
at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:227)
at org.broadinstitute.hellbender.engine.FeatureDataSource.(FeatureDataSource.java:251)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource.lambda$new$0(MultiVariantDataSource.java:89)
at java.util.ArrayList.forEach(ArrayList.java:1249)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource.(MultiVariantDataSource.java:88)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.initializeDrivingVariants(MultiVariantWalker.java:71)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:47)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:558)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.onStartup(MultiVariantWalker.java:48)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
at org.broadinstitute.hellbender.Main.main(Main.java:277)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedConstructorAccessor26.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:181)
... 16 more
Caused by: java.lang.OutOfMemoryError: Java heap space
at htsjdk.tribble.index.interval.IntervalTree.insert(IntervalTree.java:57)
at htsjdk.tribble.index.interval.IntervalTreeIndex$ChrIndex.read(IntervalTreeIndex.java:223)
at htsjdk.tribble.index.AbstractIndex.read(AbstractIndex.java:404)
at htsjdk.tribble.index.interval.IntervalTreeIndex.(IntervalTreeIndex.java:53)
at sun.reflect.GeneratedConstructorAccessor26.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:181)
at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:162)
at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:227)
at org.broadinstitute.hellbender.engine.FeatureDataSource.(FeatureDataSource.java:251)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource.lambda$new$0(MultiVariantDataSource.java:89)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource$$Lambda$59/1292784864.accept(Unknown Source)
... 12 more
The command I am running is:
java -Xmx200g -jar /exports/eddie3_homes_local/s0928794/tools/gatk-package-4.0.1.2-local.jar CombineGVCFs -R GCF_000471725.1_UMD_CASPUR_WB_2.0_genomic.fa --variant All_gvcfs.list -O combined_81.g.vcf.gz
The All_gvcfs.list contains absolute paths to 81 GVCF files of varied sizes (24-106 GB) generated by haplotycaller of GATK 4.0.1.2. Ex:
/exports/cmvm/eddie/eb/groups/prendergast_dutta_phd/WGS_atlas_animals_gvcf/Lodi_female_30x_WGS_atlas.g.vcf
/exports/cmvm/eddie/eb/groups/prendergast_dutta_phd/WGS_atlas_animals_gvcf/Pandharpuri_female_30x_WGS_atlas.g.vcf
/exports/cmvm/eddie/eb/groups/prendergast_dutta_phd/WGS_atlas_animals_gvcf/Lodi_male_30x_WGS_atlas.g.vcf
/exports/cmvm/eddie/eb/groups/prendergast_dutta_phd/WGS_atlas_animals_gvcf/Bhadawari_male_30x_WGS_atlas.g.vcf
/exports/cmvm/eddie/eb/groups/prendergast_dutta_phd/indian_wgs_10x_gvcf/Surti-214_10x.g.vcf
/exports/cmvm/eddie/eb/groups/prendergast_dutta_phd/indian_wgs_10x_gvcf/Jaffrabadi-548_10x.g.vcf
/exports/cmvm/eddie/eb/groups/prendergast_dutta_phd/indian_wgs_10x_gvcf/Bhadhwari-B254_10x.g.vcf
.....Total 81 GVCFs
I tested many java heap sizes (started from 8G, but not all files were being read by VCFCodec, when I gave 200G, it read all, but the above error came when the traversal was actually going to start.