java.lang.OutOfMemoryError: Java heap space

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Root Cause Analysis

  1. java.lang.OutOfMemoryError

    Java heap space

    at java.util.Arrays.copyOfRange()
  2. Java RT
    StringBuilder.toString
    1. java.util.Arrays.copyOfRange(Arrays.java:2694)
    2. java.lang.String.<init>(String.java:203)
    3. java.lang.StringBuilder.toString(StringBuilder.java:405)
    3 frames
  3. Scala
    StringBuilder.toString
    1. scala.collection.mutable.StringBuilder.toString(StringBuilder.scala:427)
    1 frame
  4. org.bdgenomics.avocado
    BiallelicGenotyper$$anonfun$19.apply
    1. org.bdgenomics.avocado.genotyping.BiallelicGenotyper$$anonfun$19.apply(BiallelicGenotyper.scala:403)
    2. org.bdgenomics.avocado.genotyping.BiallelicGenotyper$$anonfun$19.apply(BiallelicGenotyper.scala:393)
    2 frames
  5. Scala
    AbstractTraversable.map
    1. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
    2. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
    3. scala.collection.immutable.HashMap$HashMap1.foreach(HashMap.scala:224)
    4. scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:403)
    5. scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:403)
    6. scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:403)
    7. scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:403)
    8. scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
    9. scala.collection.AbstractTraversable.map(Traversable.scala:105)
    9 frames
  6. org.bdgenomics.avocado
    BiallelicGenotyper.updateObservations
    1. org.bdgenomics.avocado.genotyping.BiallelicGenotyper.updateObservations(BiallelicGenotyper.scala:393)
    1 frame