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

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via GitHub by fnothaft
, 1 year ago
Your input file has a malformed header: BUG: VCF header has duplicate sample names
htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: BUG: VCF header has duplicate sample names
at htsjdk.variant.vcf.VCFHeader.(VCFHeader.java:142)
at org.bdgenomics.adam.rdd.variation.VariantContextRDD.saveAsVcf(VariantContextRDD.scala:145)
at org.bdgenomics.adam.cli.ADAM2Vcf.run(ADAM2Vcf.scala:86)
at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)
at org.bdgenomics.adam.cli.ADAM2Vcf.run(ADAM2Vcf.scala:62)
at org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:132)
at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:72)
at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)

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