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)