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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Solutions on the web14517

  • 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
  • Key found in VariantContext field INFO at chr1:786343 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
  • via GitHub by hyong2000
    , 1 year ago
    Key ADP found in VariantContext field INFO at chr1:3300162 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
  • Stack trace

    • 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>(TraverseActiveRegions.java:307) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:271) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

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