htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: BUG: VCF header has duplicate sample names

GitHub | fnothaft | 8 months ago
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    GitHub comment 1179#248427561

    GitHub | 8 months ago | fnothaft
    htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: BUG: VCF header has duplicate sample names

    Root Cause Analysis

    1. htsjdk.tribble.TribbleException$InvalidHeader

      Your input file has a malformed header: BUG: VCF header has duplicate sample names

      at htsjdk.variant.vcf.VCFHeader.<init>()
    2. HTS JDK
      VCFHeader.<init>
      1. htsjdk.variant.vcf.VCFHeader.<init>(VCFHeader.java:142)
      1 frame
    3. org.bdgenomics.adam
      ADAM2Vcf.run
      1. org.bdgenomics.adam.rdd.variation.VariantContextRDD.saveAsVcf(VariantContextRDD.scala:145)
      2. org.bdgenomics.adam.cli.ADAM2Vcf.run(ADAM2Vcf.scala:86)
      2 frames
    4. org.bdgenomics.utils
      BDGSparkCommand$class.run
      1. org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)
      1 frame
    5. org.bdgenomics.adam
      ADAMMain.main
      1. org.bdgenomics.adam.cli.ADAM2Vcf.run(ADAM2Vcf.scala:62)
      2. org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:132)
      3. org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:72)
      4. org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
      4 frames
    6. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      4. java.lang.reflect.Method.invoke(Method.java:498)
      4 frames
    7. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
      2. org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
      3. org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
      4. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
      5. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      5 frames