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Error produced when running VariantAnnotator

jsheltonjshelton New YorkMember

Hi,

I have begun getting the following error when running VariantAnnotator. What does this indicate?

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

java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at java.lang.Integer.valueOf(Unknown Source)
at org.broadinstitute.variant.vcf.AbstractVCFCodec.decodeInts(AbstractVCFCodec.java:696)
at org.broadinstitute.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:655)
at org.broadinstitute.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:113)
at org.broadinstitute.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:131)
at org.broadinstitute.variant.variantcontext.LazyGenotypesContext.getGenotypes(LazyGenotypesContext.java:121)
at org.broadinstitute.variant.variantcontext.GenotypesContext.iterator(GenotypesContext.java:462)
at org.broadinstitute.variant.variantcontext.VariantContext.validateGenotypes(VariantContext.java:1233)
at org.broadinstitute.variant.variantcontext.VariantContext.validate(VariantContext.java:1175)
at org.broadinstitute.variant.variantcontext.VariantContext.(VariantContext.java:333)
at org.broadinstitute.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:478)
at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:201)
at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:177)
at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:290)
at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:82)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
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: For input string: ""
ERROR ------------------------------------------------------------------------------------------

Answers

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