Regression

org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.discover and call simple SNP and score all sites

Failing for the past 1 build (Since Failed#228 )
Took 46 sec.

Error Message

Job aborted due to stage failure: Task 5 in stage 7.0 failed 1 times, most recent failure: Lost task 5.0 in stage 7.0 (TID 410, localhost, executor driver): java.lang.OutOfMemoryError: GC overhead limit exceeded
 at java.io.ObjectStreamClass.newInstance(ObjectStreamClass.java:967)
 at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1785)
 at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
 at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1707)
 at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1345)
 at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
 at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
 at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
 at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
 at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
 at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
 at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
 at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
 at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
 at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
 at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
 at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
 at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
 at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
 at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
 at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
 at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
 at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
 at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
 at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
 at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
 at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
 at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
 at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
 at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
 at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
 at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)

Driver stacktrace:

Stacktrace

      org.apache.spark.SparkException: Job aborted due to stage failure: Task 5 in stage 7.0 failed 1 times, most recent failure: Lost task 5.0 in stage 7.0 (TID 410, localhost, executor driver): java.lang.OutOfMemoryError: GC overhead limit exceeded
	at java.io.ObjectStreamClass.newInstance(ObjectStreamClass.java:967)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1785)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
	at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1707)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1345)
	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)

Driver stacktrace:
      at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1499)
      at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1487)
      at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486)
      at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
      at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
      at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486)
      at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
      at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
      at scala.Option.foreach(Option.scala:236)
      at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
      at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1714)
      at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669)
      at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658)
      at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
      at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
      at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
      at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
      at org.apache.spark.SparkContext.runJob(SparkContext.scala:2062)
      at org.apache.spark.SparkContext.runJob(SparkContext.scala:2087)
      at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
      at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
      at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
      at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
      at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
      at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$16.apply$mcV$sp(BiallelicGenotyperSuite.scala:430)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:102)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
      at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
      at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
      at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
      at org.scalatest.Transformer.apply(Transformer.scala:22)
      at org.scalatest.Transformer.apply(Transformer.scala:20)
      at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
      at org.scalatest.Suite$class.withFixture(Suite.scala:1122)
      at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
      at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
      at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
      at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
      at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
      at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
      at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.org$scalatest$BeforeAndAfter$$super$runTest(BiallelicGenotyperSuite.scala:46)
      at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
      at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.runTest(BiallelicGenotyperSuite.scala:46)
      at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208)
      at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208)
      at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:413)
      at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:401)
      at scala.collection.immutable.List.foreach(List.scala:318)
      at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:401)
      at org.scalatest.SuperEngine.org$scalatest$SuperEngine$$runTestsInBranch(Engine.scala:396)
      at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:483)
      at org.scalatest.FunSuiteLike$class.runTests(FunSuiteLike.scala:208)
      at org.scalatest.FunSuite.runTests(FunSuite.scala:1555)
      at org.scalatest.Suite$class.run(Suite.scala:1424)
      at org.scalatest.FunSuite.org$scalatest$FunSuiteLike$$super$run(FunSuite.scala:1555)
      at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212)
      at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212)
      at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
      at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
      at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.org$scalatest$BeforeAndAfter$$super$run(BiallelicGenotyperSuite.scala:46)
      at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
      at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.run(BiallelicGenotyperSuite.scala:46)
      at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
      at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528)
      at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526)
      at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
      at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
      at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526)
      at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29)
      at org.scalatest.Suite$class.run(Suite.scala:1421)
      at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29)
      at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
      at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563)
      at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557)
      at scala.collection.immutable.List.foreach(List.scala:318)
      at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557)
      at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044)
      at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
      at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
      at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
      at org.scalatest.tools.Runner$.main(Runner.scala:860)
      at org.scalatest.tools.Runner.main(Runner.scala)
      Cause: java.lang.OutOfMemoryError: GC overhead limit exceeded
      at java.io.ObjectStreamClass.newInstance(ObjectStreamClass.java:967)
      at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1785)
      at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
      at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1707)
      at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1345)
      at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
      at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
      at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
      at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
      at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
      at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
      at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
      at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
      at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
      at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
      at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
      at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
      at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
      at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
      at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
      at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
      at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
      at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
      at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
      at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
      at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
      at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
      at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)
      at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351)
      at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000)
      at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924)
      at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801)