htsjdk.tribble.TribbleException

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