org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Alignment 60055114 | 38S113M

GitHub | malinlarsson | 3 months ago
  1. 0

    remove threading from MuTect2.

    GitHub | 3 months ago | malinlarsson
    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Alignment 60055114 | 38S113M
  2. 0

    GATK | GATK | Tagged #bug

    broadinstitute.org | 6 months ago
    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Alignment 10357 | 86M15H
  3. 0

    GATK | GATK | Tagged #bug

    broadinstitute.org | 6 months ago
    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to open index file (mark/reset not supported)000ordered.bai
  4. Speed up your debug routine!

    Automated exception search integrated into your IDE

  5. 0

    GATK | GATK | Tagged #indelrealigner

    broadinstitute.org | 6 months ago
    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: No such reader id is available

    Root Cause Analysis

    1. org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

      Somehow the requested coordinate is not covered by the read. Alignment 60055114 | 38S113M

      at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate()
    2. org.broadinstitute.gatk
      NanoScheduler$ReadMapReduceJob.run
      1. org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:580)
      2. org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:436)
      3. org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:427)
      4. org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:548)
      5. org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesRightTail(ReadClipper.java:197)
      6. org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipToRegion(ReadClipper.java:377)
      7. org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipToRegion(ReadClipper.java:352)
      8. org.broadinstitute.gatk.utils.activeregion.ActiveRegion.trim(ActiveRegion.java:482)
      9. org.broadinstitute.gatk.utils.activeregion.ActiveRegion.trim(ActiveRegion.java:437)
      10. org.broadinstitute.gatk.tools.walkers.haplotypecaller.ActiveRegionTrimmer$Result.getCallableRegion(ActiveRegionTrimmer.java:383)
      11. org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:551)
      12. org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:176)
      13. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
      14. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
      15. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
      15 frames
    3. Java RT
      Thread.run
      1. java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
      2. java.util.concurrent.FutureTask.run(FutureTask.java:266)
      3. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
      4. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
      5. java.lang.Thread.run(Thread.java:745)
      5 frames