java.lang.NoSuchMethodError: scala.collection.Seq.aggregate(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;)Ljava/lang/Object;

GitHub | zainryan | 7 months ago
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    Support spark2.0.0

    GitHub | 7 months ago | zainryan
    java.lang.NoSuchMethodError: scala.collection.Seq.aggregate(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;)Ljava/lang/Object;

    Root Cause Analysis

    1. java.lang.NoSuchMethodError

      scala.collection.Seq.aggregate(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;)Ljava/lang/Object;

      at org.bdgenomics.adam.models.NonoverlappingRegions.mergeRegions()
    2. org.bdgenomics.adam
      TwoBitFile$$anonfun$6.apply
      1. org.bdgenomics.adam.models.NonoverlappingRegions.mergeRegions(NonoverlappingRegions.scala:75)
      2. org.bdgenomics.adam.models.NonoverlappingRegions.<init>(NonoverlappingRegions.scala:55)
      3. org.bdgenomics.adam.models.NonoverlappingRegions$.apply(NonoverlappingRegions.scala:169)
      4. org.bdgenomics.adam.util.TwoBitRecord$.apply(TwoBitFile.scala:193)
      5. org.bdgenomics.adam.util.TwoBitFile$$anonfun$6.apply(TwoBitFile.scala:70)
      6. org.bdgenomics.adam.util.TwoBitFile$$anonfun$6.apply(TwoBitFile.scala:70)
      6 frames
    3. Scala
      AbstractTraversable.map
      1. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
      2. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
      3. scala.collection.immutable.HashMap$HashMap1.foreach(HashMap.scala:221)
      4. scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:428)
      5. scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:428)
      6. scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
      7. scala.collection.AbstractTraversable.map(Traversable.scala:104)
      7 frames
    4. org.bdgenomics.adam
      TwoBitFile.<init>
      1. org.bdgenomics.adam.util.TwoBitFile.<init>(TwoBitFile.scala:70)
      1 frame
    5. org.broadinstitute.hellbender
      Main.main
      1. org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSource.<init>(ReferenceTwoBitSource.java:43)
      2. org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource.<init>(ReferenceMultiSource.java:41)
      3. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:353)
      4. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:320)
      5. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:311)
      6. org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)
      7. org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108)
      8. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166)
      9. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
      10. org.broadinstitute.hellbender.Main.instanceMain(Main.java:76)
      11. org.broadinstitute.hellbender.Main.main(Main.java:92)
      11 frames
    6. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      4. java.lang.reflect.Method.invoke(Method.java:497)
      4 frames
    7. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:729)
      2. org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:185)
      3. org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:210)
      4. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:124)
      5. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      5 frames