java.lang.NumberFormatException: For input string: "0,0,0,1"

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Root Cause Analysis

  1. java.lang.NumberFormatException

    For input string: "0,0,0,1"

    at java.lang.NumberFormatException.forInputString()
  2. Java RT
    Integer.valueOf
    1. java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    2. java.lang.Integer.parseInt(Integer.java:580)
    3. java.lang.Integer.valueOf(Integer.java:766)
    3 frames
  3. org.bdgenomics.adam
    VariantAnnotationConverter$$anonfun$convert$2.apply
    1. org.bdgenomics.adam.converters.VariantAnnotationConverter$.org$bdgenomics$adam$converters$VariantAnnotationConverter$$attrAsInt(VariantAnnotationConverter.scala:76)
    2. org.bdgenomics.adam.converters.VariantAnnotationConverter$$anonfun$22.apply(VariantAnnotationConverter.scala:190)
    3. org.bdgenomics.adam.converters.VariantAnnotationConverter$$anonfun$convert$2.apply(VariantAnnotationConverter.scala:307)
    4. org.bdgenomics.adam.converters.VariantAnnotationConverter$$anonfun$convert$2.apply(VariantAnnotationConverter.scala:303)
    4 frames
  4. Scala
    TraversableLike$WithFilter.foreach
    1. scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:772)
    2. scala.collection.immutable.Map$Map4.foreach(Map.scala:181)
    3. scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:771)
    3 frames
  5. org.bdgenomics.adam
    VariantContextConverter$$anonfun$6.apply
    1. org.bdgenomics.adam.converters.VariantAnnotationConverter$.convert(VariantAnnotationConverter.scala:303)
    2. org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$6.apply(VariantContextConverter.scala:406)
    3. org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$6.apply(VariantContextConverter.scala:386)
    3 frames
  6. Scala
    AbstractTraversable.map
    1. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
    2. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
    3. scala.collection.Iterator$class.foreach(Iterator.scala:727)
    4. scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
    5. scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
    6. scala.collection.AbstractIterable.foreach(Iterable.scala:54)
    7. scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
    8. scala.collection.AbstractTraversable.map(Traversable.scala:105)
    8 frames
  7. org.bdgenomics.adam
    ADAMContext$$anonfun$loadVcf$1.apply
    1. org.bdgenomics.adam.converters.VariantContextConverter.extractGenotypes(VariantContextConverter.scala:385)
    2. org.bdgenomics.adam.converters.VariantContextConverter.extractReferenceModelGenotypes(VariantContextConverter.scala:471)
    3. org.bdgenomics.adam.converters.VariantContextConverter.convert(VariantContextConverter.scala:210)
    4. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
    5. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
    5 frames
  8. Scala
    Iterator$$anon$13.hasNext
    1. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
    1 frame
  9. Spark
    Executor$TaskRunner.run
    1. org.apache.spark.util.Utils$.getIteratorSize(Utils.scala:1595)
    2. org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157)
    3. org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157)
    4. org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858)
    5. org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858)
    6. org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
    7. org.apache.spark.scheduler.Task.run(Task.scala:89)
    8. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
    8 frames
  10. 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