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

Google Groups | Jaeki Hong | 2 years ago
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    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