java.lang.reflect.InvocationTargetException

GitHub | kwongj | 4 months ago
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  1. 0

    GitHub comment 2#252799348

    GitHub | 4 months ago | kwongj
    java.lang.reflect.InvocationTargetException
  2. 0

    unpaired broken with v1.15

    GitHub | 1 year ago | tolot27
    java.lang.reflect.InvocationTargetException
  3. 0

    IllegalStateException

    GitHub | 1 year ago | arefeen
    java.lang.IllegalStateException: Inappropriate call if not paired read
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  5. 0

    samcompare supporting single-end reads

    GitHub | 2 years ago | wx115
    java.lang.IllegalStateException: Inappropriate call if not paired read
  6. 0

    GitHub comment 16#183133735

    GitHub | 1 year ago | shenkers
    java.lang.IllegalStateException: Inappropriate call if not paired read

    Root Cause Analysis

    1. java.lang.IllegalStateException

      Inappropriate call if not paired read

      at htsjdk.samtools.SAMRecord.requireReadPaired()
    2. HTS JDK
      SAMRecord.getFirstOfPairFlag
      1. htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:648)
      2. htsjdk.samtools.SAMRecord.getFirstOfPairFlag(SAMRecord.java:706)
      2 frames
    3. org.broadinstitute.pilon
      BamFile$MateMap$$anonfun$addReads$1.apply
      1. org.broadinstitute.pilon.BamFile$MateMap.addRead(BamFile.scala:224)
      2. org.broadinstitute.pilon.BamFile$MateMap$$anonfun$addReads$1.apply(BamFile.scala:220)
      3. org.broadinstitute.pilon.BamFile$MateMap$$anonfun$addReads$1.apply(BamFile.scala:220)
      3 frames
    4. Scala
      List.foreach
      1. scala.collection.immutable.List.foreach(List.scala:381)
      1 frame
    5. org.broadinstitute.pilon
      GapFiller$$anonfun$recruitReadsOfType$1.apply
      1. org.broadinstitute.pilon.BamFile$MateMap.addReads(BamFile.scala:220)
      2. org.broadinstitute.pilon.BamFile$MateMap.<init>(BamFile.scala:218)
      3. org.broadinstitute.pilon.BamFile.recruitFlankReads(BamFile.scala:339)
      4. org.broadinstitute.pilon.GapFiller$$anonfun$recruitReadsOfType$1.apply(GapFiller.scala:367)
      5. org.broadinstitute.pilon.GapFiller$$anonfun$recruitReadsOfType$1.apply(GapFiller.scala:366)
      5 frames
    6. Scala
      List.foreach
      1. scala.collection.immutable.List.foreach(List.scala:381)
      1 frame
    7. org.broadinstitute.pilon
      GenomeRegion$$anonfun$identifyAndFixIssues$4.apply
      1. org.broadinstitute.pilon.GapFiller.recruitReadsOfType(GapFiller.scala:366)
      2. org.broadinstitute.pilon.GapFiller.recruitFrags(GapFiller.scala:375)
      3. org.broadinstitute.pilon.GapFiller.recruitLocalReads(GapFiller.scala:389)
      4. org.broadinstitute.pilon.GapFiller.recruitReads(GapFiller.scala:391)
      5. org.broadinstitute.pilon.GapFiller.assembleAcrossBreak(GapFiller.scala:51)
      6. org.broadinstitute.pilon.GapFiller.fixBreak(GapFiller.scala:45)
      7. org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:381)
      8. org.broadinstitute.pilon.GenomeRegion$$anonfun$identifyAndFixIssues$4.apply(GenomeRegion.scala:379)
      8 frames
    8. Scala
      List.foreach
      1. scala.collection.immutable.List.foreach(List.scala:381)
      1 frame
    9. org.broadinstitute.pilon
      GenomeFile$$anonfun$processRegions$4.apply
      1. org.broadinstitute.pilon.GenomeRegion.identifyAndFixIssues(GenomeRegion.scala:379)
      2. org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:120)
      3. org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:109)
      3 frames
    10. Scala
      ForkJoinWorkerThread.run
      1. scala.collection.Iterator$class.foreach(Iterator.scala:893)
      2. scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
      3. scala.collection.parallel.ParIterableLike$Foreach.leaf(ParIterableLike.scala:972)
      4. scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
      5. scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
      6. scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
      7. scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
      8. scala.collection.parallel.ParIterableLike$Foreach.tryLeaf(ParIterableLike.scala:969)
      9. scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:152)
      10. scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
      11. scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
      12. scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
      13. scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
      14. scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
      15. scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
      15 frames