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

broadinstitute.org | 6 months ago
tip
Your exception is missing from the Samebug knowledge base.
Here are the best solutions we found on the Internet.
Click on the to mark the helpful solution and get rewards for you help.
  1. 0

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

    broadinstitute.org | 1 year ago
    java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
  2. 0

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

    broadinstitute.org | 6 months ago
    java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
  3. 0

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

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

    Automated exception search integrated into your IDE

  5. 0

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

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

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

    broadinstitute.org | 10 hours 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:997)
      9. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:779)
      10. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:290)
      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