java.lang.NumberFormatException: For input string: "."

broadinstitute.org | 7 months ago
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    java.lang.NumberFormatException: For input string: "."

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Root Cause Analysis

  1. java.lang.NumberFormatException

    For input string: "."

    at sun.misc.FloatingDecimal.readJavaFormatString()
  2. Java RT
    Double.parseDouble
    1. sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1250)
    2. java.lang.Double.parseDouble(Double.java:540)
    2 frames
  3. HTS JDK
    IndexFactory.createDynamicIndex
    1. htsjdk.variant.variantcontext.GenotypeLikelihoods.parseDeprecatedGLString(GenotypeLikelihoods.java:251)
    2. htsjdk.variant.variantcontext.GenotypeLikelihoods.fromGLField(GenotypeLikelihoods.java:81)
    3. htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:715)
    4. htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:128)
    5. htsjdk.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:158)
    6. htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:347)
    7. htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279)
    8. htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257)
    9. htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60)
    10. htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
    11. htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
    12. htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:40)
    13. htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:502)
    14. htsjdk.tribble.index.IndexFactory$FeatureIterator.<init>(IndexFactory.java:403)
    15. htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:312)
    15 frames
  4. org.broadinstitute.gatk
    CommandLineGATK.main
    1. org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:401)
    2. org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:287)
    3. org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:224)
    4. org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:147)
    5. org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.<init>(ReferenceOrderedDataSource.java:208)
    6. org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.<init>(ReferenceOrderedDataSource.java:88)
    7. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:1047)
    8. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:828)
    9. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
    10. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    11. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    12. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    13. org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
    13 frames