java.lang.OutOfMemoryError

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  • GitHub comment 572#249369489
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  • OOM error
    via GitHub by jpdna
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    • java.lang.OutOfMemoryError: Java heap space at java.util.IdentityHashMap.resize(IdentityHashMap.java:471) at java.util.IdentityHashMap.put(IdentityHashMap.java:440) at org.apache.spark.util.SizeEstimator$SearchState.enqueue(SizeEstimator.scala:176) at org.apache.spark.util.SizeEstimator$$anonfun$visitSingleObject$1.apply(SizeEstimator.scala:224) at org.apache.spark.util.SizeEstimator$$anonfun$visitSingleObject$1.apply(SizeEstimator.scala:223) at scala.collection.immutable.List.foreach(List.scala:318) at org.apache.spark.util.SizeEstimator$.visitSingleObject(SizeEstimator.scala:223) at org.apache.spark.util.SizeEstimator$.org$apache$spark$util$SizeEstimator$$estimate(SizeEstimator.scala:203) at org.apache.spark.util.SizeEstimator$.estimate(SizeEstimator.scala:70) at org.apache.spark.util.collection.SizeTracker$class.takeSample(SizeTracker.scala:78) at org.apache.spark.util.collection.SizeTracker$class.afterUpdate(SizeTracker.scala:70) at org.apache.spark.util.collection.SizeTrackingVector.$plus$eq(SizeTrackingVector.scala:31) at org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:285) at org.apache.spark.storage.MemoryStore.putIterator(MemoryStore.scala:169) at org.apache.spark.storage.MemoryStore.putIterator(MemoryStore.scala:147) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:798) at org.apache.spark.storage.BlockManager.putIterator(BlockManager.scala:645) at org.apache.spark.storage.BlockManager.putSingle(BlockManager.scala:1003) at org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:99) at org.apache.spark.broadcast.TorrentBroadcast.<init>(TorrentBroadcast.scala:85) at org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:34) at org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:63) at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1326) at org.hammerlab.guacamole.readsets.rdd.PartitionedRegions$.compute(PartitionedRegions.scala:199) at org.hammerlab.guacamole.readsets.rdd.PartitionedRegions$.apply(PartitionedRegions.scala:184) at org.hammerlab.guacamole.readsets.rdd.PartitionedRegions$.apply(PartitionedRegions.scala:146) at org.hammerlab.guacamole.commands.SomaticJoint$.makeCalls(SomaticJointCaller.scala:166) at org.hammerlab.guacamole.commands.SomaticJoint$Caller$.run(SomaticJointCaller.scala:91) at org.hammerlab.guacamole.commands.SomaticJoint$Caller$.run(SomaticJointCaller.scala:56) at org.hammerlab.guacamole.commands.SparkCommand.run(SparkCommand.scala:12) at org.hammerlab.guacamole.commands.Command.run(Command.scala:27) at org.hammerlab.guacamole.Main$.main(Main.scala:49)

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