GenotypeGVCFs java error; java.lang.NegativeArraySizeException

goodstorygoodstory Seoul, KoreaMember
edited November 2016 in Ask the GATK team

Hello!
I used the following command to run GATK GenotypeGVCFs.
(GATK version : nightly-2016-11-23-g69e703d / Java : Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14)

======================================================================
java -Xmx100g -jar /home/opt/GATK/3.6-nightly-2016-11-23/GenomeAnalysisTK.jar \
-T GenotypeGVCFs \
-R /home/resource/reference/human/UCSC/hg38/BWAIndex/genome.fa \
-L chrY \
-o /scratch/GATK/gVCF/WGSproject.chrY.vcf \
--variant /scratch/GATK/gVCF/WGSproject.v1.chrY.part0.g.vcf \
--variant /scratch/GATK/gVCF/WGSproject.v1.chrY.part1.g.vcf \
--variant /scratch/GATK/gVCF/WGSproject.v1.chrY.part2.g.vcf \
--variant /scratch/GATK/gVCF/WGSproject.v1.chrY.part3.g.vcf \
--variant /scratch/GATK/gVCF/WGSproject.v1.chrY.part4.g.vcf \

--variant /scratch/GATK/gVCF/AdditionalSample.chrY.Haplotype.raw.snps.g.vcf

*Over 400 samples were collected in units of 100 units by combineGVCFs (size : 25~35GB) + 1 addiation sample (size : 120GB)

As a result, the following error occurs :

ERROR --
ERROR stack trace

java.lang.NegativeArraySizeException
at htsjdk.tribble.readers.AsciiLineReader.readLine(AsciiLineReader.java:103)
at htsjdk.tribble.readers.AsciiLineReader.readLine(AsciiLineReader.java:122)
at htsjdk.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator
.java:86)
at htsjdk.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator
.java:75)
at htsjdk.samtools.util.AbstractIterator.next(AbstractIterator.java:57)
at htsjdk.tribble.readers.AsciiLineReaderIterator.next(AsciiLineReaderIterator.java:48)
at htsjdk.tribble.readers.AsciiLineReaderIterator.next(AsciiLineReaderIterator.java:26)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:74)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:36)
at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:518)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:480)
at htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:354)
at htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:317)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBui
lder.java:441)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:
327)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilde
r.java:264)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackB
uilder.java:153)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(Referenc
eOrderedDataSource.java:208)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOr
deredDataSource.java:88)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAna
lysisEngine.java:1052)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngi
ne.java:829)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:287)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:2
56)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:1
58)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version nightly-2016-11-23-g69e703d):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem

.

ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)

##### ERROR ------------------------------------------------------------------------------------------

Perhaps it is the error that is related to the index file, and the same error occurs after deleting all of the indexs.

How do you solve this problem?

Answers

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