java.lang.IllegalStateException: Rod span chr1:1-249250621 isn't contained within the data shard chr1:1-249250621, meaning we wouldn't get all of the data we need

broadinstitute.org | 7 days ago
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    broadinstitute.org | 7 days ago
    java.lang.IllegalStateException: Rod span chr1:1-249250621 isn't contained within the data shard chr1:1-249250621, meaning we wouldn't get all of the data we need
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    broadinstitute.org | 8 months ago
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    Root Cause Analysis

    1. java.lang.IllegalStateException

      Rod span chr1:1-249250621 isn't contained within the data shard chr1:1-249250621, meaning we wouldn't get all of the data we need

      at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.<init>()
    2. org.broadinstitute.gatk
      CommandLineGATK.main
      1. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.<init>(TraverseActiveRegions.java:307)
      2. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:271)
      3. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
      4. org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
      5. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
      6. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
      7. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
      8. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
      9. org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
      9 frames