java.lang.IllegalArgumentException: At least one constraint must be defined for the EM algorithm.

Google Groups | Jaeki Hong | 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

    How should I define EM algorithm in Avocado configuration?

    Google Groups | 2 years ago | Jaeki Hong
    java.lang.IllegalArgumentException: At least one constraint must be defined for the EM algorithm.

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      At least one constraint must be defined for the EM algorithm.

      at org.bdgenomics.avocado.genotyping.BiallelicGenotyper$.apply()
    2. org.bdgenomics.avocado
      CallGenotypes$$anonfun$apply$1$$anonfun$apply$4.apply
      1. org.bdgenomics.avocado.genotyping.BiallelicGenotyper$.apply(BiallelicGenotyper.scala:72)
      2. org.bdgenomics.avocado.genotyping.GenotyperCompanion$class.apply(Genotyper.scala:38)
      3. org.bdgenomics.avocado.genotyping.BiallelicGenotyper$.apply(BiallelicGenotyper.scala:43)
      4. org.bdgenomics.avocado.genotyping.CallGenotypes$$anonfun$apply$1$$anonfun$apply$4.apply(CallGenotypes.scala:40)
      5. org.bdgenomics.avocado.genotyping.CallGenotypes$$anonfun$apply$1$$anonfun$apply$4.apply(CallGenotypes.scala:40)
      5 frames
    3. Scala
      Option.fold
      1. scala.Option.fold(Option.scala:157)
      1 frame
    4. org.bdgenomics.avocado
      CallGenotypes$$anonfun$apply$1.apply
      1. org.bdgenomics.avocado.genotyping.CallGenotypes$$anonfun$apply$1.apply(CallGenotypes.scala:40)
      2. org.bdgenomics.avocado.genotyping.CallGenotypes$$anonfun$apply$1.apply(CallGenotypes.scala:43)
      2 frames
    5. Spark
      Timer.time
      1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
      1 frame
    6. org.bdgenomics.avocado
      Avocado$$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$1.apply(Avocado.scala:148)
      3 frames
    7. Spark
      Timer.time
      1. org.apache.spark.rdd.Timer.time(Timer.scala:57)
      1 frame
    8. org.bdgenomics.avocado
      Avocado.run
      1. org.bdgenomics.avocado.cli.Avocado.callVariants(Avocado.scala:148)
      2. org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:213)
      2 frames
    9. org.bdgenomics.adam
      ADAMSparkCommand$class.run
      1. org.bdgenomics.adam.cli.ADAMSparkCommand$class.run(ADAMCommand.scala:57)
      1 frame
    10. org.bdgenomics.avocado
      Avocado.run
      1. org.bdgenomics.avocado.cli.Avocado.run(Avocado.scala:81)
      1 frame
    11. org.bdgenomics.adam
      ADAMCommandCompanion$class.main
      1. org.bdgenomics.adam.cli.ADAMCommandCompanion$class.main(ADAMCommand.scala:35)
      1 frame
    12. org.bdgenomics.avocado
      Avocado.main
      1. org.bdgenomics.avocado.cli.Avocado$.main(Avocado.scala:51)
      2. org.bdgenomics.avocado.cli.Avocado.main(Avocado.scala)
      2 frames
    13. 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
    14. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:358)
      2. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:75)
      3. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      3 frames