java.lang.OutOfMemoryError: GC overhead limit exceeded

GitHub | car2008 | 3 months ago
  1. 0

    GitHub comment 572#246607309

    GitHub | 3 months ago | car2008
    java.lang.OutOfMemoryError: GC overhead limit exceeded
  2. 0

    Picard SamToFastq problem : Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit - GATK-Forum

    broadinstitute.org | 11 months ago
    java.lang.OutOfMemoryError: GC overhead limit exceeded
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    Root Cause Analysis

    1. java.lang.OutOfMemoryError

      GC overhead limit exceeded

      at htsjdk.samtools.BinaryTagCodec.readTags()
    2. HTS JDK
      SAMRecord.getReadGroup
      1. htsjdk.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:282)
      2. htsjdk.samtools.BAMRecord.decodeAttributes(BAMRecord.java:308)
      3. htsjdk.samtools.BAMRecord.getAttribute(BAMRecord.java:288)
      4. htsjdk.samtools.SAMRecord.getReadGroup(SAMRecord.java:691)
      4 frames
    3. org.hammerlab.guacamole
      ReadSets$$anonfun$8.apply
      1. org.hammerlab.guacamole.reads.Read$.apply(Read.scala:77)
      2. org.hammerlab.guacamole.readsets.ReadSets$$anonfun$8.apply(ReadSets.scala:276)
      3. org.hammerlab.guacamole.readsets.ReadSets$$anonfun$8.apply(ReadSets.scala:266)
      3 frames
    4. Scala
      AbstractTraversable.toArray
      1. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
      2. scala.collection.Iterator$class.toStream(Iterator.scala:1143)
      3. scala.collection.AbstractIterator.toStream(Iterator.scala:1157)
      4. scala.collection.Iterator$$anonfun$toStream$1.apply(Iterator.scala:1143)
      5. scala.collection.Iterator$$anonfun$toStream$1.apply(Iterator.scala:1143)
      6. scala.collection.immutable.Stream$Cons.tail(Stream.scala:1085)
      7. scala.collection.immutable.Stream$Cons.tail(Stream.scala:1077)
      8. scala.collection.immutable.Stream.length(Stream.scala:284)
      9. scala.collection.SeqLike$class.size(SeqLike.scala:106)
      10. scala.collection.AbstractSeq.size(Seq.scala:40)
      11. scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:248)
      12. scala.collection.AbstractTraversable.toArray(Traversable.scala:105)
      12 frames
    5. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.ParallelCollectionRDD$.slice(ParallelCollectionRDD.scala:154)
      2. org.apache.spark.rdd.ParallelCollectionRDD.getPartitions(ParallelCollectionRDD.scala:97)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    6. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    7. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    8. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    9. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      3 frames