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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Solutions on the web16602

  • via GitHub by jpdna
    , 8 months ago
    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
  • BUG: Cannot add a no call allele to a variant context [TA*, .] this=[VC Unknown @ chr1:53707-53708 Q584.04 of type=INDEL alleles=[TA*, .] attr={CONC_ST=[EMPTY]} GT=[[call ./. DP 1 AD 1,0],[truth ./. DP 1 AD 1,0]]
  • counts [WP=3 WN=0 WB=0 WR=1 WQ=0 WK=1][BP=0 BN= 0 BB=0 BR=1 BQ=0 BK=1] |_|_|k|_|_|_|_|_| Moves: 85 EP: - Castle: - |_|_|_|_|_|_|_|P| FEN: 3R4/3P4/2k5/7P/6K1/6P1/8/7r b - - 0 43 |_|_|_|_|_|_|K|_| State: 3072 Variant=lightning Result=0-1
  • Stack trace

    • 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(VariantContextConverter.scala:214) at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823) at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823) at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371) at org.apache.spark.util.Utils$.getIteratorSize(Utils.scala:1595) at org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157) at org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) at org.apache.spark.scheduler.Task.run(Task.scala:89) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)

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