{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/2113","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2113/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2113/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2113/events","html_url":"https://github.com/broadinstitute/gatk/issues/2113","id":173031057,"number":2113,"title":"Failure on SparkGenomeReadCounts (addProbabilisticSplits)","user":{"login":"achevali","id":6088871,"avatar_url":"https://avatars.githubusercontent.com/u/6088871?v=3","gravatar_id":"","url":"https://api.github.com/users/achevali","html_url":"https://github.com/achevali","followers_url":"https://api.github.com/users/achevali/followers","following_url":"https://api.github.com/users/achevali/following{/other_user}","gists_url":"https://api.github.com/users/achevali/gists{/gist_id}","starred_url":"https://api.github.com/users/achevali/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/achevali/subscriptions","organizations_url":"https://api.github.com/users/achevali/orgs","repos_url":"https://api.github.com/users/achevali/repos","events_url":"https://api.github.com/users/achevali/events{/privacy}","received_events_url":"https://api.github.com/users/achevali/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-08-24T18:57:41Z","updated_at":"2016-08-25T19:33:33Z","closed_at":null,"body":"Attempting to get wgs coverage with 10000 bp bin size on\r\n/seq/picard_aggregation/D4491/HCC1143/v1/HCC1143.bam\r\nproduces the following stacktrace (see first line for command line)\r\n```\r\nERROR 14:06:46,283 FunctionEdge - Error: java -Xmx16g -jar /dsde/working/slee/acnv-eval/resources/gatk-protected-536b94e-create-apon.jar SparkGenomeReadCounts -o /dsde/working/aaronc/testing/case/HCC1143/cov/HCC1143-coverage.tsv -I /seq/picard_aggregation/D4491/HCC1143/v1/HCC1143.bam -bins 10000 -R /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta --sparkMaster local[1] \r\nERROR 14:06:46,288 FunctionEdge - Contents of /dsde/working/aaronc/testing/case/HCC1143/cov/HCC1143-coverage.tsv.out:\r\n16/08/24 14:06:09 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.2 KB, free 284.6 KB)\r\n16/08/24 14:06:09 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on localhost:56998 (size: 23.2 KB, free: 10.4 GB)\r\n16/08/24 14:06:09 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ReadsSparkSource.java:105\r\n16/08/24 14:06:10 INFO FileInputFormat: Total input paths to process : 1\r\n16/08/24 14:06:21 INFO SparkUI: Stopped Spark web UI at http://10.200.98.30:4040\r\n16/08/24 14:06:21 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!\r\n16/08/24 14:06:21 INFO MemoryStore: MemoryStore cleared\r\n16/08/24 14:06:21 INFO BlockManager: BlockManager stopped\r\n16/08/24 14:06:21 INFO BlockManagerMaster: BlockManagerMaster stopped\r\n16/08/24 14:06:21 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!\r\n16/08/24 14:06:21 INFO SparkContext: Successfully stopped SparkContext\r\n14:06:21.109 INFO  SparkGenomeReadCounts - Shutting down engine\r\n[August 24, 2016 2:06:21 PM EDT] org.broadinstitute.hellbender.tools.genome.SparkGenomeReadCounts done. Elapsed time: 0.36 minutes.\r\nRuntime.totalMemory()=3192389632\r\njava.lang.IndexOutOfBoundsException\r\n\tat java.nio.ByteBuffer.wrap(ByteBuffer.java:375)\r\n\tat htsjdk.samtools.BAMRecord.getCigar(BAMRecord.java:246)\r\n\tat org.seqdoop.hadoop_bam.BAMSplitGuesser.guessNextBAMRecordStart(BAMSplitGuesser.java:189)\r\n\tat org.seqdoop.hadoop_bam.BAMInputFormat.addProbabilisticSplits(BAMInputFormat.java:244)\r\n\tat org.seqdoop.hadoop_bam.BAMInputFormat.getSplits(BAMInputFormat.java:159)\r\n\tat org.seqdoop.hadoop_bam.AnySAMInputFormat.getSplits(AnySAMInputFormat.java:253)\r\n\tat org.apache.spark.rdd.NewHadoopRDD.getPartitions(NewHadoopRDD.scala:120)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)\r\n\tat scala.Option.getOrElse(Option.scala:120)\r\n\tat org.apache.spark.rdd.RDD.partitions(RDD.scala:237)\r\n\tat org.apache.spark.Partitioner$.defaultPartitioner(Partitioner.scala:65)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$reduceByKey$3.apply(PairRDDFunctions.scala:331)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$reduceByKey$3.apply(PairRDDFunctions.scala:331)\r\n\tat org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)\r\n\tat org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)\r\n\tat org.apache.spark.rdd.RDD.withScope(RDD.scala:316)\r\n\tat org.apache.spark.rdd.PairRDDFunctions.reduceByKey(PairRDDFunctions.scala:330)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:381)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:381)\r\n\tat org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)\r\n\tat org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)\r\n\tat org.apache.spark.rdd.RDD.withScope(RDD.scala:316)\r\n\tat org.apache.spark.rdd.PairRDDFunctions.countByKey(PairRDDFunctions.scala:380)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1187)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1187)\r\n\tat org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)\r\n\tat org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)\r\n\tat org.apache.spark.rdd.RDD.withScope(RDD.scala:316)\r\n\tat org.apache.spark.rdd.RDD.countByValue(RDD.scala:1186)\r\n\tat org.apache.spark.api.java.JavaRDDLike$class.countByValue(JavaRDDLike.scala:461)\r\n\tat org.apache.spark.api.java.AbstractJavaRDDLike.countByValue(JavaRDDLike.scala:46)\r\n\tat org.broadinstitute.hellbender.tools.genome.SparkGenomeReadCounts.collectReads(SparkGenomeReadCounts.java:134)\r\n\tat org.broadinstitute.hellbender.tools.genome.SparkGenomeReadCounts.runTool(SparkGenomeReadCounts.java:213)\r\n\tat org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:313)\r\n\tat org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)\r\n\tat org.broadinstitute.hellbender.Main.instanceMain(Main.java:76)\r\n\tat org.broadinstitute.hellbender.Main.main(Main.java:92)\r\n```"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/242510056","html_url":"https://github.com/broadinstitute/gatk/issues/2113#issuecomment-242510056","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2113","id":242510056,"user":{"login":"achevali","id":6088871,"avatar_url":"https://avatars.githubusercontent.com/u/6088871?v=3","gravatar_id":"","url":"https://api.github.com/users/achevali","html_url":"https://github.com/achevali","followers_url":"https://api.github.com/users/achevali/followers","following_url":"https://api.github.com/users/achevali/following{/other_user}","gists_url":"https://api.github.com/users/achevali/gists{/gist_id}","starred_url":"https://api.github.com/users/achevali/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/achevali/subscriptions","organizations_url":"https://api.github.com/users/achevali/orgs","repos_url":"https://api.github.com/users/achevali/repos","events_url":"https://api.github.com/users/achevali/events{/privacy}","received_events_url":"https://api.github.com/users/achevali/received_events","type":"User","site_admin":false},"created_at":"2016-08-25T19:33:33Z","updated_at":"2016-08-25T19:33:33Z","body":"ValidateSamFile shows no errors with the bam."}}
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