Java NumberFormatException?

KOOLKATKOOLKAT Member
edited October 2012 in Ask the GATK team

I am working on calling snps from raw fastq files. I use GATK as part of my pipeline and I found it great.
While I was working on some other files, this error occured.(from RealignerTargetCreater)

INFO 21:12:03,374 TraversalEngine - 3:40841007 5.33e+08 9.0 m 1.0 s 17.2% 52.4 m 43.4 m
INFO 21:12:33,270 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.NumberFormatException: For input string: "6451478"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:481)
at java.lang.Integer.valueOf(Integer.java:570)
at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:316)
at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:287)
at org.broad.tribble.source.BasicFeatureSource$IteratorImpl.readNextRecord(BasicFeatureSource.java:296)
at org.broad.tribble.source.BasicFeatureSource$IteratorImpl.next(BasicFeatureSource.java:346)
at org.broad.tribble.source.BasicFeatureSource$IteratorImpl.next(BasicFeatureSource.java:251)
at org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator.next(FeatureToGATKFeatureIterator.java:58)
at org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator.next(FeatureToGATKFeatureIterator.java:40)
at org.broadinstitute.sting.gatk.iterators.PushbackIterator.next(PushbackIterator.java:49)
at org.broadinstitute.sting.gatk.refdata.SeekableRODIterator.seekForward(SeekableRODIterator.java:331)
at org.broadinstitute.sting.gatk.datasources.providers.ManagingReferenceOrderedView.getReferenceOrderedDataAtLocus(ManagingReferenceOrderedView.java:59)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:74)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:248)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.6-11-g3b2fab9):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: For input string: "6451478"
ERROR ------------------------------------------------------------------------------------------

I believe it is some kind of input error, but still I can't figure out what is problem.
Any idea?

Answers

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