java.lang.RuntimeException: java.lang.reflect.InvocationTargetException

broadinstitute.org | 2 months ago
  1. 0

    VariantAnnotator, GATK3.2 Error "java.lang.reflect.InvocationTargetException". Ubuntu 12 java 1.7. - GATK-Forum

    broadinstitute.org | 12 months ago
    java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
  2. 0

    VariantAnnotator, GATK3.2 Error "java.lang.reflect.InvocationTargetException". Ubuntu 12 java 1.7. — GATK-Forum

    broadinstitute.org | 2 months ago
    java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
  3. 0

    ERROR MESSAGE: java.lang.reflect.InvocationTargetException - GATK-Forum

    broadinstitute.org | 12 months ago
    java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
  4. Speed up your debug routine!

    Automated exception search integrated into your IDE

  5. 0

    ERROR MESSAGE: java.lang.reflect.InvocationTargetException — GATK-Forum

    broadinstitute.org | 1 month ago
    java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
  6. 0

    java.lang.reflect.InvocationTargetException — GATK-Forum

    broadinstitute.org | 3 days ago
    java.lang.RuntimeException: java.lang.reflect.InvocationTargetException

    Not finding the right solution?
    Take a tour to get the most out of Samebug.

    Tired of useless tips?

    Automated exception search integrated into your IDE

    Root Cause Analysis

    1. java.io.EOFException

      No message provided

      at htsjdk.tribble.util.LittleEndianInputStream.readFully()
    2. HTS JDK
      LinearIndex.<init>
      1. htsjdk.tribble.util.LittleEndianInputStream.readFully(LittleEndianInputStream.java:138)
      2. htsjdk.tribble.util.LittleEndianInputStream.readLong(LittleEndianInputStream.java:80)
      3. htsjdk.tribble.index.linear.LinearIndex$ChrIndex.read(LinearIndex.java:271)
      4. htsjdk.tribble.index.AbstractIndex.read(AbstractIndex.java:363)
      5. htsjdk.tribble.index.linear.LinearIndex.<init>(LinearIndex.java:101)
      5 frames
    3. Java RT
      Constructor.newInstance
      1. sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      2. sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
      3. sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      4. java.lang.reflect.Constructor.newInstance(Constructor.java:526)
      4 frames
    4. HTS JDK
      IndexFactory.loadIndex
      1. htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:185)
      1 frame
    5. org.broadinstitute.gatk
      CommandLineGATK.main
      1. org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:336)
      2. org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:320)
      3. org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:279)
      4. org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:225)
      5. org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:148)
      6. org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.<init>(ReferenceOrderedDataSource.java:208)
      7. org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.<init>(ReferenceOrderedDataSource.java:88)
      8. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:990)
      9. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:772)
      10. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:285)
      11. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
      12. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
      13. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
      14. org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
      14 frames