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

broadinstitute.org | 5 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

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

    broadinstitute.org | 5 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?
  2. 0

    GATK | GATK | Blog

    broadinstitute.org | 7 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 | 1 year ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (3942) > (39) STOP -- this should never happen -- call Mauricio!
  4. Speed up your debug routine!

    Automated exception search integrated into your IDE

  5. 0

    GATK | GATK | Tagged #gatk

    broadinstitute.org | 11 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 | 11 months ago
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Too many deletions?

    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. 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