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

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  • GitHub comment 1179#248427561
    via GitHub by fnothaft
    ,
    • htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: BUG: VCF header has duplicate sample names at htsjdk.variant.vcf.VCFHeader.<init>(VCFHeader.java:142) at org.bdgenomics.adam.rdd.variation.VariantContextRDD.saveAsVcf(VariantContextRDD.scala:145) at org.bdgenomics.adam.cli.ADAM2Vcf.run(ADAM2Vcf.scala:86) at org.bdgenomics.utils.cli.BDGSparkCommand$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) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
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