Error Stack trace after running SelectVariants
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I just wanted to select variants from a VCF with 42 samples. After 3 hours I got the following Error. How to fix this? please advise. Thanks I had the same problem when I used "VQSR". How can I fix this problem?

INFO 20:28:17,247 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:28:17,250 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-4-g6f46d11, Compiled 2013/10/10 17:27:51 INFO 20:28:17,250 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 20:28:17,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 20:28:17,255 HelpFormatter - Program Args: -T SelectVariants -rf BadCigar -R /groups/body/JDM_RNA_Seq-2012/GATK/bundle-2.3/ucsc.hg19/ucsc.hg19.fasta -V /hms/scratch1/mahyar/Danny/data/Overal-RGSM-42prebamfiles-allsites.vcf -L chr1 -L chr2 -L chr3 -selectType SNP -o /hms/scratch1/mahyar/Danny/data/Filter/extract_SNP_only3chr.vcf INFO 20:28:17,256 HelpFormatter - Date/Time: 2014/01/20 20:28:17 INFO 20:28:17,256 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:28:17,256 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:28:17,305 ArgumentTypeDescriptor - Dynamically determined type of /hms/scratch1/mahyar/Danny/data/Overal-RGSM-42prebamfiles-allsites.vcf to be VCF INFO 20:28:18,053 GenomeAnalysisEngine - Strictness is SILENT INFO 20:28:18,167 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 20:28:18,188 RMDTrackBuilder - Creating Tribble index in memory for file /hms/scratch1/mahyar/Danny/data/Overal-RGSM-42prebamfiles-allsites.vcf INFO 23:15:08,278 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NegativeArraySizeException at org.broad.tribble.readers.AsciiLineReader.readLine(AsciiLineReader.java:97) at org.broad.tribble.readers.AsciiLineReader.readLine(AsciiLineReader.java:116) at org.broad.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator.java:84) at org.broad.tribble.readers.AsciiLineReaderIterator$TupleIterator.advance(AsciiLineReaderIterator.java:73) at net.sf.samtools.util.AbstractIterator.next(AbstractIterator.java:57) at org.broad.tribble.readers.AsciiLineReaderIterator.next(AsciiLineReaderIterator.java:46) at org.broad.tribble.readers.AsciiLineReaderIterator.next(AsciiLineReaderIterator.java:24) at org.broad.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:73) at org.broad.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:35) at org.broad.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:40) at org.broad.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:428) at org.broad.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:390) at org.broad.tribble.index.IndexFactory.createIndex(IndexFactory.java:288) at org.broad.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:278) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:388) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:274) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:211) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:140) at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208) at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:964) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:758) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:284) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.7-4-g6f46d11):
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

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