org.apache.spark.SparkException: Job aborted due to stage failure: Task 2 in stage 6.0 failed 1 times, most recent failure: Lost task 2.0 in stage 6.0 (TID 42, localhost): java.lang.NoSuchMethodError: breeze.linalg.sum$.sumSummableThings(Lscala/Predef$$less$colon$less;Lbreeze/generic/UFunc$UImpl2;)Lbreeze/generic/UFunc$UImpl;

GitHub | ryan-williams | 2 months ago
  1. 0

    Breeze NoSuchMethodError

    GitHub | 2 months ago | ryan-williams
    org.apache.spark.SparkException: Job aborted due to stage failure: Task 2 in stage 6.0 failed 1 times, most recent failure: Lost task 2.0 in stage 6.0 (TID 42, localhost): java.lang.NoSuchMethodError: breeze.linalg.sum$.sumSummableThings(Lscala/Predef$$less$colon$less;Lbreeze/generic/UFunc$UImpl2;)Lbreeze/generic/UFunc$UImpl;
  2. 0

    Error on executing 'Select * from tablename'

    GitHub | 1 year ago | rkiyer999
    org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 6.0 failed 1 times, most recent failure: Lost task 0.0 in stage 6.0 (TID 6, localhost): java.lang.ArrayIndexOutOfBoundsException: 1
  3. 0

    Not possible to change column names

    GitHub | 10 months ago | arkadiuszbicz
    org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 6.0 failed 1 times, most recent failure: Lost task 0.0 in stage 6.0 (TID 7, localhost): java.lang.NegativeArraySizeException
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  5. 0

    exception thrown on worker gets "Task exception could not be deserialized" ClassNotFoundException error

    Stack Overflow | 8 months ago | Cotton Seed
    org.apache.spark.SparkException: Job aborted due to stage failure: Task 6 in stage 1.0 failed 1 times, most recent failure: Lost task 6.0 in stage 1.0 (TID 14, localhost): org.apache.spark.SparkException: oops
  6. 0

    Spark throws Exception when constructing Dataframe

    Stack Overflow | 1 month ago | Bindumalini KK
    org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 2.0 failed 1 times, most recent failure: Lost task 0.0 in stage 2.0 (TID 2, localhost): java.lang.NullPointerException

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    Root Cause Analysis

    1. org.apache.spark.SparkException

      Job aborted due to stage failure: Task 2 in stage 6.0 failed 1 times, most recent failure: Lost task 2.0 in stage 6.0 (TID 42, localhost): java.lang.NoSuchMethodError: breeze.linalg.sum$.sumSummableThings(Lscala/Predef$$less$colon$less;Lbreeze/generic/UFunc$UImpl2;)Lbreeze/generic/UFunc$UImpl;

      at org.hammerlab.guacamole.likelihood.Likelihood$$anonfun$4.apply()
    2. org.hammerlab.guacamole
      Likelihood$$anonfun$4.apply
      1. org.hammerlab.guacamole.likelihood.Likelihood$$anonfun$4.apply(Likelihood.scala:161)
      2. org.hammerlab.guacamole.likelihood.Likelihood$$anonfun$4.apply(Likelihood.scala:156)
      2 frames
    3. Scala
      ArrayOps$ofRef.map
      1. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
      2. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
      3. scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
      4. scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
      5. scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
      6. scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:108)
      6 frames
    4. org.hammerlab.guacamole
      WindowFlatMapUtils$$anonfun$splitPartitionByContigAndMap$2.apply
      1. org.hammerlab.guacamole.likelihood.Likelihood$.likelihoodsOfGenotypes(Likelihood.scala:156)
      2. org.hammerlab.guacamole.likelihood.Likelihood$.likelihoodsOfAllPossibleGenotypesFromPileup(Likelihood.scala:78)
      3. org.hammerlab.guacamole.commands.SomaticStandard$Caller$.findPotentialVariantAtLocus(SomaticStandardCaller.scala:182)
      4. org.hammerlab.guacamole.commands.SomaticStandard$Caller$$anonfun$1.apply(SomaticStandardCaller.scala:95)
      5. org.hammerlab.guacamole.commands.SomaticStandard$Caller$$anonfun$1.apply(SomaticStandardCaller.scala:94)
      6. org.hammerlab.guacamole.distributed.PileupFlatMapUtils$$anonfun$pileupFlatMapTwoSamples$1.apply(PileupFlatMapUtils.scala:84)
      7. org.hammerlab.guacamole.distributed.PileupFlatMapUtils$$anonfun$pileupFlatMapTwoSamples$1.apply(PileupFlatMapUtils.scala:79)
      8. org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$windowFlatMapWithState$1$$anonfun$apply$1.apply(WindowFlatMapUtils.scala:65)
      9. org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$windowFlatMapWithState$1$$anonfun$apply$1.apply(WindowFlatMapUtils.scala:55)
      10. org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$splitPartitionByContigAndMap$2.apply(WindowFlatMapUtils.scala:141)
      11. org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$splitPartitionByContigAndMap$2.apply(WindowFlatMapUtils.scala:131)
      11 frames
    5. Scala
      Iterator$$anon$13.hasNext
      1. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
      1 frame
    6. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:284)
      2. org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171)
      3. org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78)
      4. org.apache.spark.rdd.RDD.iterator(RDD.scala:268)
      5. org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
      6. org.apache.spark.scheduler.Task.run(Task.scala:89)
      7. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
      7 frames
    7. Java RT
      Thread.run
      1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
      2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
      3. java.lang.Thread.run(Thread.java:745)
      3 frames