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

Searched on Google with the first line of a JAVA stack trace?

We can recommend more relevant solutions and speed up debugging when you paste your entire stack trace with the exception message. Try a sample exception.

Recommended solutions based on your search

Solutions on the web

via Google Groups by someya sayeh, 10 months ago
org.bdgenomics.formats.avro.Fragment cannot be cast to
java.lang.ClassCastException: org.bdgenomics.formats.avro.Fragment cannot be cast to
at org.bdgenomics.adam.rdd.variation.GenotypeRDDFunctions$$anonfun$10.apply(VariationRDDFunctions.scala:153)
at org.apache.spark.rdd.RDD$$anonfun$keyBy$1.apply(RDD.scala:1324)
at org.apache.spark.rdd.RDD$$anonfun$keyBy$1.apply(RDD.scala:1324)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
at org.apache.spark.util.collection.ExternalSorter.spillToPartitionFiles(ExternalSorter.scala:371)
at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:211)
at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:63)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:64)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1204)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1193)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1192)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:693)
at scala.Option.foreach(Option.scala:236)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:693)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1393)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1354)

Users with the same issue

You are the first who have seen this exception. Write a tip to help other users and build your expert profile.

Know the solutions? Share your knowledge to help other developers to debug faster.