java.lang.NoSuchMethodError: org.apache.spark.rdd.OrderedRDDFunctions.repartitionAndSortWithinPartitions(Lorg/apache/spark/P artitioner;)Lorg/apache/spark/rdd/RDD;

Google Groups | Sungwook Yoon | 2 years ago
tip
Your exception is missing from the Samebug knowledge base.
Here are the best solutions we found on the Internet.
Click on the to mark the helpful solution and get rewards for you help.
  1. 0

    error in avocado

    Google Groups | 2 years ago | Sungwook Yoon
    java.lang.NoSuchMethodError: org.apache.spark.rdd.OrderedRDDFunctions.repartitionAndSortWithinPartitions(Lorg/apache/spark/P artitioner;)Lorg/apache/spark/rdd/RDD;
  2. 0

    avocado-submit not working? - Failure at step "groupby at BiallelicGenotyper.Scala"

    Google Groups | 2 years ago | Unknown author
    java.lang.NoSuchMethodError: org.apache.spark.rdd.OrderedRDDFunctions.repartitionAndSortWithinPartitions(Lorg/apache/spark/Partitioner;)Lorg/apache/spark/rdd/RDD;

    Root Cause Analysis

    1. java.lang.NoSuchMethodError

      org.apache.spark.rdd.OrderedRDDFunctions.repartitionAndSortWithinPartitions(Lorg/apache/spark/P artitioner;)Lorg/apache/spark/rdd/RDD;

      at org.bdgenomics.avocado.genotyping.BiallelicGenotyper.genotype()
    2. org.bdgenomics.avocado
      CallGenotypes$$anonfun$apply$1.apply
      1. org.bdgenomics.avocado.genotyping.BiallelicGenotyper.genotype(BiallelicGenotyper.scala:369)
      2. org.bdgenomics.avocado.genotyping.CallGenotypes$$anonfun$apply$1.apply(CallGenotypes.scala:43)
      3. org.bdgenomics.avocado.genotyping.CallGenotypes$$anonfun$apply$1.apply(CallGenotypes.scala:43)
      3 frames
    3. Spark
      Timer.time
      1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
      1 frame
    4. org.bdgenomics.avocado
      Avocado$$anonfun$callVariants$1.apply
      1. org.bdgenomics.avocado.genotyping.CallGenotypes$.apply(CallGenotypes.scala:36)
      2. org.bdgenomics.avocado.cli.Avocado$$anonfun$callVariants$1.apply(Avocado.scala:154)
      3. org.bdgenomics.avocado.cli.Avocado$$anonfun$callVariants$1.apply(Avocado.scala:148)
      3 frames
    5. Spark
      Timer.time
      1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
      1 frame
    6. org.bdgenomics.avocado
      Avocado.run
      1. org.bdgenomics.avocado.cli.Avocado.callVariants(Avocado.scala:148)
      2. org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:213)
      2 frames
    7. org.bdgenomics.adam
      ADAMSparkCommand$class.run
      1. org.bdgenomics.adam.cli.ADAMSparkCommand$class.run(ADAMCommand.scala:57)
      1 frame
    8. org.bdgenomics.avocado
      Avocado.run
      1. org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:81)
      1 frame
    9. org.bdgenomics.adam
      ADAMCommandCompanion$class.main
      1. org.bdgenomics.adam.cli.ADAMCommandCompanion$class.main(ADAMCommand.scala:35)
      1 frame
    10. org.bdgenomics.avocado
      Avocado.main
      1. org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:51)
      2. org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
      2 frames
    11. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      4. java.lang.reflect.Method.invoke(Method.java:606)
      4 frames
    12. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:328)
      2. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:75)
      3. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      3 frames