org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?

broadinstitute.org | 2 months ago
  1. 0

    BaseRecalibrator: Array length mismatch detected. Malformed read — GATK-Forum

    broadinstitute.org | 2 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?
  2. 0

    GATK | GATK | Blog

    broadinstitute.org | 4 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (3942) > (39) STOP -- this should never happen -- call Mauricio!
  3. 0

    Bug in various tools, 2.4-7 : "ArrayIndexOutOfBoundsException" - GATK-Forum

    broadinstitute.org | 11 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (3942) > (39) STOP -- this should never happen -- call Mauricio!
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  5. 0

    GATK | GATK | Tagged #gatk

    broadinstitute.org | 8 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Too many deletions?
  6. 0

    GATK | GATK | Tagged #unifiedgenotyper

    broadinstitute.org | 8 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Too many deletions?

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    Root Cause Analysis

    1. org.broadinstitute.sting.utils.exceptions.ReviewedStingException

      Array length mismatch detected. Malformed read?

      at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateFractionalErrorArray()
    2. org.broadinstitute.sting
      CommandLineGATK.main
      1. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateFractionalErrorArray(BaseRecalibrator.java:371)
      2. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:246)
      3. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
      4. org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
      5. org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
      6. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287)
      7. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252)
      8. org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
      9. org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
      10. org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
      11. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
      12. org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
      13. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
      14. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
      15. org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
      15 frames