java.lang.NullPointerException

Google Groups | Unknown author | 1 year ago
tip
Click on the to mark the solution that helps you, Samebug will learn from it.
As a community member, you’ll be rewarded for you help.

Root Cause Analysis

  1. java.lang.NullPointerException

    No message provided

    at org.bdgenomics.adam.rich.RichAlignmentRecord.qualityScores$lzycompute()
  2. org.bdgenomics.adam
    RichAlignmentRecord.qualityScores
    1. org.bdgenomics.adam.rich.RichAlignmentRecord.qualityScores$lzycompute(RichAlignmentRecord.scala:75)
    2. org.bdgenomics.adam.rich.RichAlignmentRecord.qualityScores(RichAlignmentRecord.scala:74)
    2 frames
  3. org.bdgenomics.avocado
    ReadExplorer$$anonfun$readToObservations$1.apply
    1. org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$readToObservations$1.apply(ReadExplorer.scala:66)
    2. org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$readToObservations$1.apply(ReadExplorer.scala:46)
    2 frames
  4. Spark
    Timer.time
    1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
    1 frame
  5. org.bdgenomics.avocado
    ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply
    1. org.bdgenomics.avocado.discovery.ReadExplorer.readToObservations(ReadExplorer.scala:46)
    2. org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply(ReadExplorer.scala:177)
    3. org.bdgenomics.avocado.discovery.ReadExplorer$$anonfun$discover$1$$anonfun$apply$3.apply(ReadExplorer.scala:177)
    3 frames
  6. Scala
    Iterator$$anon$11.hasNext
    1. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
    2. scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
    3. scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
    3 frames
  7. Spark
    Executor$TaskRunner.run
    1. org.apache.spark.util.collection.ExternalSorter.spillToPartitionFiles(ExternalSorter.scala:365)
    2. org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:211)
    3. org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:63)
    4. org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
    5. org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
    6. org.apache.spark.scheduler.Task.run(Task.scala:64)
    7. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:203)
    7 frames
  8. Java RT
    Thread.run
    1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    3. java.lang.Thread.run(Thread.java:745)
    3 frames