java.lang.ClassCastException: org.apache.avro.generic.GenericData$Recor d cannot be cast to org.bdgenomics.formats.avro.NucleotideContigFragment

Google Groups | Sungwook Yoon | 2 years ago
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  1. 0

    avocado error reading adam files

    Google Groups | 2 years ago | Sungwook Yoon
    java.lang.ClassCastException: org.apache.avro.generic.GenericData$Recor d cannot be cast to org.bdgenomics.formats.avro.NucleotideContigFragment
  2. 0

    avocado class cast error

    Google Groups | 2 years ago | Sungwook Yoon
    java.lang.ClassCastException: org.apache.avro.generic.GenericData$Record cannot be cast to org.bdgenomics.formats.avro.NucleotideContigFragment

    Root Cause Analysis

    1. java.lang.ClassCastException

      org.apache.avro.generic.GenericData$Recor d cannot be cast to org.bdgenomics.formats.avro.NucleotideContigFragment

      at org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentRDDFunctions.getSequenceRecordsFromElement()
    2. org.bdgenomics.adam
      ADAMSequenceDictionaryRDDAggregator$$anonfun$2.apply
      1. org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentRDDFunctions.getSequenceRecordsFromElement(NucleotideContigFragmentRDDFunctions.scala:39)
      2. org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator.org$bdgenomics$adam$rdd$ADAMSequenceDictionaryRDDAggregator$$mergeRecords$1(ADAMRDDFunctions.scala:105)
      3. org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator$$anonfun$2.apply(ADAMRDDFunctions.scala:117)
      4. org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator$$anonfun$2.apply(ADAMRDDFunctions.scala:117)
      4 frames
    3. Scala
      AbstractIterator.foldLeft
      1. scala.collection.TraversableOnce$$anonfun$foldLeft$1.apply(TraversableOnce.scala:144)
      2. scala.collection.TraversableOnce$$anonfun$foldLeft$1.apply(TraversableOnce.scala:144)
      3. scala.collection.Iterator$class.foreach(Iterator.scala:727)
      4. scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
      5. scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:144)
      6. scala.collection.AbstractIterator.foldLeft(Iterator.scala:1157)
      6 frames
    4. org.bdgenomics.adam
      ADAMSequenceDictionaryRDDAggregator$$anonfun$adamGetSequenceDictionary$1.apply
      1. org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator.org$bdgenomics$adam$rdd$ADAMSequenceDictionaryRDDAggregator$$foldIterator$1(ADAMRDDFunctions.scala:117)
      2. org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator$$anonfun$adamGetSequenceDictionary$1.apply(ADAMRDDFunctions.scala:121)
      3. org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator$$anonfun$adamGetSequenceDictionary$1.apply(ADAMRDDFunctions.scala:121)
      3 frames
    5. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.rdd.RDD$$anonfun$14.apply(RDD.scala:634)
      2. org.apache.spark.rdd.RDD$$anonfun$14.apply(RDD.scala:634)
      3. org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
      4. org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
      5. org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
      6. org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
      7. org.apache.spark.scheduler.Task.run(Task.scala:64)
      8. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:203)
      8 frames
    6. 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