java.lang.ClassCastException: org.bdgenomics.formats.avro.Fragment cannot be cast to

Google Groups | someya sayeh | 11 months ago
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    adam2vcf

    Google Groups | 11 months ago | someya sayeh
    java.lang.ClassCastException: org.bdgenomics.formats.avro.Fragment cannot be cast to

    Root Cause Analysis

    1. java.lang.ClassCastException

      org.bdgenomics.formats.avro.Fragment cannot be cast to

      at org.bdgenomics.adam.rdd.variation.GenotypeRDDFunctions$$anonfun$10.apply()
    2. org.bdgenomics.adam
      GenotypeRDDFunctions$$anonfun$10.apply
      1. org.bdgenomics.adam.rdd.variation.GenotypeRDDFunctions$$anonfun$10.apply(VariationRDDFunctions.scala:153)
      1 frame
    3. Spark
      RDD$$anonfun$keyBy$1.apply
      1. org.apache.spark.rdd.RDD$$anonfun$keyBy$1.apply(RDD.scala:1324)
      2. org.apache.spark.rdd.RDD$$anonfun$keyBy$1.apply(RDD.scala:1324)
      2 frames
    4. Scala
      Iterator$$anon$11.next
      1. scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
      2. scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
      2 frames
    5. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.util.collection.ExternalSorter.spillToPartitionFiles(ExternalSorter.scala:371)
      2. org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:211)
      3. org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:63)
      4. org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
      5. org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
      6. org.apache.spark.scheduler.Task.run(Task.scala:64)
      7. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:203)
      7 frames
    6. Java RT
      Thread.run
      1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
      2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
      3. java.lang.Thread.run(Thread.java:745)
      3 frames
    7. Spark
      DAGScheduler$$anonfun$abortStage$1.apply
      1. org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1204)
      2. org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1193)
      3. org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1192)
      3 frames
    8. Scala
      ArrayBuffer.foreach
      1. scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
      2. scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
      2 frames
    9. Spark
      DAGScheduler$$anonfun$handleTaskSetFailed$1.apply
      1. org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1192)
      2. org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:693)
      3. org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:693)
      3 frames
    10. Scala
      Option.foreach
      1. scala.Option.foreach(Option.scala:236)
      1 frame
    11. Spark
      EventLoop$$anon$1.run
      1. org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:693)
      2. org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1393)
      3. org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1354)
      4. org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
      4 frames