htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing

GitHub | ooliynyk | 6 months ago
tip
Click on the to mark the solution that helps you, Samebug will learn from it.
As a community member, you’ll be rewarded for you help.
  1. 0

    vcf2adam unparsable vcf record

    GitHub | 6 months ago | ooliynyk
    htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing
  2. 0

    Investigate failures to load ExAC.0.3.GRCh38.vcf variants

    GitHub | 1 month ago | heuermh
    htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 15364: Duplicate allele added to VariantContext: C
  3. 0

    GitHub comment 1114#252664902

    GitHub | 4 months ago | heuermh
    java.util.concurrent.ExecutionException: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 21: The VCF specification requires a valid filter status: filter was
  4. Speed up your debug routine!

    Automated exception search integrated into your IDE

    Root Cause Analysis

    1. htsjdk.tribble.TribbleException

      The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing

      at htsjdk.variant.vcf.AbstractVCFCodec.generateException()
    2. HTS JDK
      AbstractVCFCodec.decode
      1. htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:783)
      2. htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:572)
      3. htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:531)
      4. htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336)
      5. htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279)
      6. htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257)
      6 frames
    3. org.seqdoop.hadoop_bam
      VCFRecordReader.nextKeyValue
      1. org.seqdoop.hadoop_bam.VCFRecordReader.nextKeyValue(VCFRecordReader.java:144)
      1 frame
    4. Spark
      InterruptibleIterator.hasNext
      1. org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:163)
      2. org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
      2 frames
    5. Scala
      Iterator$$anon$11.hasNext
      1. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
      2. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
      3. scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
      3 frames
    6. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp(PairRDDFunctions.scala:1034)
      2. org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply(PairRDDFunctions.scala:1034)
      3. org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply(PairRDDFunctions.scala:1034)
      4. org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1206)
      5. org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1042)
      6. org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1014)
      7. org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
      8. org.apache.spark.scheduler.Task.run(Task.scala:88)
      9. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
      9 frames
    7. 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