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Importing directory of VCFs seems to fail #898

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fnothaft opened this Issue Dec 18, 2015 · 1 comment

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fnothaft commented Dec 18, 2015

Reported by @almussel while trying to sort out some dbSNP input stuff:

Exception in thread "main" htsjdk.tribble.TribbleException: Input stream does not contain a BCF encoded file; BCF magic header info not found, at record 0 with position 0:
at htsjdk.variant.bcf2.BCF2Codec.error(BCF2Codec.java:492)
at htsjdk.variant.bcf2.BCF2Codec.readHeader(BCF2Codec.java:153)
at org.seqdoop.hadoop_bam.BCFSplitGuesser.<init>(BCFSplitGuesser.java:107)
at org.seqdoop.hadoop_bam.BCFSplitGuesser.<init>(BCFSplitGuesser.java:88)
at org.seqdoop.hadoop_bam.VCFInputFormat.addGuessedSplits(VCFInputFormat.java:254)
at org.seqdoop.hadoop_bam.VCFInputFormat.fixBCFSplits(VCFInputFormat.java:242)
at org.seqdoop.hadoop_bam.VCFInputFormat.getSplits(VCFInputFormat.java:221)
at org.apache.spark.rdd.NewHadoopRDD.getPartitions(NewHadoopRDD.scala:115)
at org.apache.spark.rdd.RDD$anonfun$partitions$2.apply(RDD.scala:239)
at org.apache.spark.rdd.RDD$anonfun$partitions$2.apply(RDD.scala:237)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$anonfun$partitions$2.apply(RDD.scala:239)
at org.apache.spark.rdd.RDD$anonfun$partitions$2.apply(RDD.scala:237)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$anonfun$partitions$2.apply(RDD.scala:239)
at org.apache.spark.rdd.RDD$anonfun$partitions$2.apply(RDD.scala:237)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$anonfun$partitions$2.apply(RDD.scala:239)
at org.apache.spark.rdd.RDD$anonfun$partitions$2.apply(RDD.scala:237)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1914)
at org.apache.spark.rdd.PairRDDFunctions$anonfun$saveAsNewAPIHadoopDataset$1.apply$mcV$sp(PairRDDFunctions.scala:1055)
at org.apache.spark.rdd.PairRDDFunctions$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:998)
at org.apache.spark.rdd.PairRDDFunctions$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:998)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:310)
at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopDataset(PairRDDFunctions.scala:998)
at org.apache.spark.rdd.PairRDDFunctions$anonfun$saveAsNewAPIHadoopFile$2.apply$mcV$sp(PairRDDFunctions.scala:938)
at org.apache.spark.rdd.PairRDDFunctions$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:930)
at org.apache.spark.rdd.PairRDDFunctions$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:930)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:310)
at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopFile(PairRDDFunctions.scala:930)
at org.apache.spark.rdd.InstrumentedPairRDDFunctions.saveAsNewAPIHadoopFile(InstrumentedPairRDDFunctions.scala:487)
at org.bdgenomics.adam.rdd.ADAMRDDFunctions$anonfun$adamParquetSave$1.apply$mcV$sp(ADAMRDDFunctions.scala:75)
at org.bdgenomics.adam.rdd.ADAMRDDFunctions$anonfun$adamParquetSave$1.apply(ADAMRDDFunctions.scala:60)
at org.bdgenomics.adam.rdd.ADAMRDDFunctions$anonfun$adamParquetSave$1.apply(ADAMRDDFunctions.scala:60)
at org.apache.spark.rdd.Timer.time(Timer.scala:57)
at org.bdgenomics.adam.rdd.ADAMRDDFunctions.adamParquetSave(ADAMRDDFunctions.scala:60)
at org.bdgenomics.adam.rdd.ADAMRDDFunctions.adamParquetSave(ADAMRDDFunctions.scala:46)
at org.bdgenomics.adam.cli.Vcf2ADAM.run(Vcf2ADAM.scala:79)
at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:54)
at org.bdgenomics.adam.cli.Vcf2ADAM.run(Vcf2ADAM.scala:58)
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fnothaft Jan 7, 2016

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This is resolved; there was an error when copying the data over which led to some of the VCFs being headerless.

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fnothaft commented Jan 7, 2016

This is resolved; there was an error when copying the data over which led to some of the VCFs being headerless.

@fnothaft fnothaft closed this Jan 7, 2016

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