java.lang.IllegalArgumentException: Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3

GitHub | jpdna | 4 months ago
  1. 0

    gVCF - can't load multi-allelic sites

    GitHub | 4 months ago | jpdna
    java.lang.IllegalArgumentException: Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3
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    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3

      at org.bdgenomics.adam.converters.VariantContextConverter.convert()
    2. org.bdgenomics.adam
      ADAMContext$$anonfun$loadVcf$1.apply
      1. org.bdgenomics.adam.converters.VariantContextConverter.convert(VariantContextConverter.scala:214)
      2. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
      3. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
      3 frames
    3. Scala
      Iterator$$anon$13.hasNext
      1. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
      1 frame
    4. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.util.Utils$.getIteratorSize(Utils.scala:1595)
      2. org.apache.spark.rdd.RDD$$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
    5. 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