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via GitHub by heuermh
, 1 year ago
/Users/heuermh/working/adam/sorted.adam/part-r-00000.gz.parquet invalid: all the files must be contained in the root sorted.adam
org.apache.parquet.io.ParquetEncodingException: /Users/heuermh/working/adam/sorted.adam/part-r-00000.gz.parquet invalid: all the files must be contained in the root sorted.adam	at org.apache.parquet.hadoop.ParquetFileWriter.mergeFooters(ParquetFileWriter.java:444)	at org.apache.parquet.hadoop.ParquetFileWriter.writeMetadataFile(ParquetFileWriter.java:420)	at org.apache.parquet.hadoop.ParquetOutputCommitter.writeMetaDataFile(ParquetOutputCommitter.java:58)	at org.apache.parquet.hadoop.ParquetOutputCommitter.commitJob(ParquetOutputCommitter.java:48)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply$mcV$sp(PairRDDFunctions.scala:1145)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1074)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1074)	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)	at org.apache.spark.rdd.RDD.withScope(RDD.scala:316)	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopDataset(PairRDDFunctions.scala:1074)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply$mcV$sp(PairRDDFunctions.scala:994)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:985)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:985)	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)	at org.apache.spark.rdd.RDD.withScope(RDD.scala:316)	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopFile(PairRDDFunctions.scala:985)	at org.apache.spark.rdd.InstrumentedPairRDDFunctions.saveAsNewAPIHadoopFile(InstrumentedPairRDDFunctions.scala:477)	at org.bdgenomics.adam.rdd.ADAMRDDFunctions$$anonfun$saveRddAsParquet$1.apply$mcV$sp(ADAMRDDFunctions.scala:159)	at org.bdgenomics.adam.rdd.ADAMRDDFunctions$$anonfun$saveRddAsParquet$1.apply(ADAMRDDFunctions.scala:143)	at org.bdgenomics.adam.rdd.ADAMRDDFunctions$$anonfun$saveRddAsParquet$1.apply(ADAMRDDFunctions.scala:143)	at scala.Option.fold(Option.scala:157)	at org.apache.spark.rdd.Timer.time(Timer.scala:48)	at org.bdgenomics.adam.rdd.ADAMRDDFunctions.saveRddAsParquet(ADAMRDDFunctions.scala:143)	at org.bdgenomics.adam.rdd.AvroGenomicRDD.saveAsParquet(GenomicRDD.scala:908)	at org.bdgenomics.adam.rdd.AvroGenomicRDD.saveAsParquet(GenomicRDD.scala:883)	at org.bdgenomics.adam.cli.Vcf2ADAM.run(Vcf2ADAM.scala:74)	at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)	at org.bdgenomics.adam.cli.Vcf2ADAM.run(Vcf2ADAM.scala:53)	at org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:128)	at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:68)	at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)	at java.lang.reflect.Method.invoke(Method.java:497)	at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731)	at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)	at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)	at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)	at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)