java.lang.IndexOutOfBoundsException

There are no available Samebug tips for this exception. Do you have an idea how to solve this issue? A short tip would help users who saw this issue last week.

  • GitHub comment 1566#238864313
    via GitHub by slivne
    ,
  • GitHub comment 210#290973765
    via GitHub by gquerret
    ,
  • ERB parsing in JRuby 1.6.6
    via GitHub by hartjus
    ,
    • java.lang.IndexOutOfBoundsException at java.nio.ByteBuffer.wrap(ByteBuffer.java:375) at htsjdk.samtools.BAMRecord.getCigar(BAMRecord.java:246) at org.seqdoop.hadoop_bam.BAMSplitGuesser.guessNextBAMRecordStart(BAMSplitGuesser.java:189) at org.seqdoop.hadoop_bam.BAMInputFormat.addProbabilisticSplits(BAMInputFormat.java:244) at org.seqdoop.hadoop_bam.BAMInputFormat.getSplits(BAMInputFormat.java:159) at org.seqdoop.hadoop_bam.AnySAMInputFormat.getSplits(AnySAMInputFormat.java:253) at org.apache.spark.rdd.NewHadoopRDD.getPartitions(NewHadoopRDD.scala:120) 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.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.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$2.apply(RDD.scala:237) at scala.Option.getOrElse(Option.scala:120) at org.apache.spark.rdd.RDD.partitions(RDD.scala:237) at org.apache.spark.Partitioner$.defaultPartitioner(Partitioner.scala:65) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$reduceByKey$3.apply(PairRDDFunctions.scala:331) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$reduceByKey$3.apply(PairRDDFunctions.scala:331) at org.apache.spark.rdd.RDDOperationScope$.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.reduceByKey(PairRDDFunctions.scala:330) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:381) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:381) at org.apache.spark.rdd.RDDOperationScope$.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.countByKey(PairRDDFunctions.scala:380) at org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1187) at org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1187) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111) at org.apache.spark.rdd.RDD.withScope(RDD.scala:316) at org.apache.spark.rdd.RDD.countByValue(RDD.scala:1186) at org.apache.spark.api.java.JavaRDDLike$class.countByValue(JavaRDDLike.scala:461) at org.apache.spark.api.java.AbstractJavaRDDLike.countByValue(JavaRDDLike.scala:46) at org.broadinstitute.hellbender.tools.genome.SparkGenomeReadCounts.collectReads(SparkGenomeReadCounts.java:134) at org.broadinstitute.hellbender.tools.genome.SparkGenomeReadCounts.runTool(SparkGenomeReadCounts.java:213) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:313) at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:76) at org.broadinstitute.hellbender.Main.main(Main.java:92)
    No Bugmate found.