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

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  • 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 at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.bdgenomics.adam.rdd.GenomicRDD$$anonfun$12.apply(GenomicRDD.scala:219) at org.bdgenomics.adam.rdd.GenomicRDD$$anonfun$12.apply(GenomicRDD.scala:169) at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710) at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306) at org.apache.spark.rdd.RDD.iterator(RDD.scala:270) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306) at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:69) at org.apache.spark.rdd.RDD.iterator(RDD.scala:268) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) at org.apache.spark.scheduler.Task.run(Task.scala:89) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:227) 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) Caused by: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 21: The VCF specification requires a valid filter status: filter was at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:783) at htsjdk.variant.vcf.VCFCodec.parseFilters(VCFCodec.java:138) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:319) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at org.bdgenomics.adam.rdd.variation.VCFOutFormatter.convertIterator$1(VCFOutFormatter.scala:60) at org.bdgenomics.adam.rdd.variation.VCFOutFormatter.read(VCFOutFormatter.scala:66) at org.bdgenomics.adam.rdd.OutFormatterRunner.call(OutFormatter.scala:27) at org.bdgenomics.adam.rdd.OutFormatterRunner.call(OutFormatter.scala:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) ... 3 more
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