FailedConsole Output

Skipping 103 KB.. Full Log
park.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
2019-09-07 17:40:29 ERROR MapOutputTrackerMaster:91 - Error communicating with MapOutputTracker
java.lang.NullPointerException
	at org.apache.spark.MapOutputTracker.askTracker(MapOutputTracker.scala:102)
	at org.apache.spark.MapOutputTracker.getStatuses(MapOutputTracker.scala:204)
	at org.apache.spark.MapOutputTracker.getMapSizesByExecutorId(MapOutputTracker.scala:144)
	at org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:49)
	at org.apache.spark.sql.execution.ShuffledRowRDD.compute(ShuffledRowRDD.scala:165)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
2019-09-07 17:40:29 ERROR TaskContextImpl:91 - Error in TaskCompletionListener
java.lang.IllegalStateException: Block broadcast_9 not found
	at org.apache.spark.storage.BlockInfoManager$$anonfun$2.apply(BlockInfoManager.scala:293)
	at org.apache.spark.storage.BlockInfoManager$$anonfun$2.apply(BlockInfoManager.scala:293)
	at scala.Option.getOrElse(Option.scala:120)
	at org.apache.spark.storage.BlockInfoManager.unlock(BlockInfoManager.scala:292)
	at org.apache.spark.storage.BlockManager.releaseLock(BlockManager.scala:720)
	at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$releaseLock$1.apply(TorrentBroadcast.scala:250)
	at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$releaseLock$1.apply(TorrentBroadcast.scala:250)
	at org.apache.spark.TaskContext$$anon$1.onTaskCompletion(TaskContext.scala:128)
	at org.apache.spark.TaskContextImpl$$anonfun$markTaskCompleted$1.apply(TaskContextImpl.scala:117)
	at org.apache.spark.TaskContextImpl$$anonfun$markTaskCompleted$1.apply(TaskContextImpl.scala:117)
	at org.apache.spark.TaskContextImpl$$anonfun$invokeListeners$1.apply(TaskContextImpl.scala:130)
	at org.apache.spark.TaskContextImpl$$anonfun$invokeListeners$1.apply(TaskContextImpl.scala:128)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.TaskContextImpl.invokeListeners(TaskContextImpl.scala:128)
	at org.apache.spark.TaskContextImpl.markTaskCompleted(TaskContextImpl.scala:116)
	at org.apache.spark.scheduler.Task.run(Task.scala:118)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
2019-09-07 17:40:29 WARN  NettyRpcEnv:66 - RpcEnv already stopped.
- discover and call het and hom snps *** FAILED ***
  org.apache.spark.SparkException: Job aborted due to stage failure: Task 3 in stage 7.0 failed 1 times, most recent failure: Lost task 3.0 in stage 7.0 (TID 562, localhost, executor driver): java.lang.IllegalStateException: unread block data
	at java.io.ObjectInputStream$BlockDataInputStream.setBlockDataMode(ObjectInputStream.java:2783)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1605)
	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2287)
	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2211)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2069)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1573)
	at java.io.ObjectInputStream.readObject(ObjectInputStream.java:431)
	at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:75)
	at org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:114)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:80)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

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$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486)
  at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
  at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
  at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486)
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
  at scala.Option.foreach(Option.scala:256)
  at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1714)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658)
  at org.apache.spark.util.EventLoop$$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$20.apply$mcV$sp(BiallelicGenotyperSuite.scala:500)
  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:381)
  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$$anonfun$runNestedSuites$1.apply(Suite.scala:1526)
  at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
  at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186)
  at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526)
  at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29)
  at org.scalatest.Suite$class.run(Suite.scala:1421)
  at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29)
  at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557)
  at scala.collection.immutable.List.foreach(List.scala:381)
  at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
  Cause: java.lang.IllegalStateException: unread block data
  at java.io.ObjectInputStream$BlockDataInputStream.setBlockDataMode(ObjectInputStream.java:2783)
  at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1605)
  at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2287)
  at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2211)
  at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2069)
  at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1573)
  at java.io.ObjectInputStream.readObject(ObjectInputStream.java:431)
  at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:75)
  at org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:114)
  at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:80)
  at org.apache.spark.scheduler.Task.run(Task.scala:108)
  at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
  at java.lang.Thread.run(Thread.java:748)
2019-09-07 17:40:29 ERROR TaskContextImpl:91 - Error in TaskCompletionListener
java.lang.IllegalStateException: Block broadcast_9 not found
	at org.apache.spark.storage.BlockInfoManager$$anonfun$2.apply(BlockInfoManager.scala:293)
	at org.apache.spark.storage.BlockInfoManager$$anonfun$2.apply(BlockInfoManager.scala:293)
	at scala.Option.getOrElse(Option.scala:120)
	at org.apache.spark.storage.BlockInfoManager.unlock(BlockInfoManager.scala:292)
	at org.apache.spark.storage.BlockManager.releaseLock(BlockManager.scala:720)
	at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$releaseLock$1.apply(TorrentBroadcast.scala:250)
	at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$releaseLock$1.apply(TorrentBroadcast.scala:250)
	at org.apache.spark.TaskContext$$anon$1.onTaskCompletion(TaskContext.scala:128)
	at org.apache.spark.TaskContextImpl$$anonfun$markTaskCompleted$1.apply(TaskContextImpl.scala:117)
	at org.apache.spark.TaskContextImpl$$anonfun$markTaskCompleted$1.apply(TaskContextImpl.scala:117)
	at org.apache.spark.TaskContextImpl$$anonfun$invokeListeners$1.apply(TaskContextImpl.scala:130)
	at org.apache.spark.TaskContextImpl$$anonfun$invokeListeners$1.apply(TaskContextImpl.scala:128)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.TaskContextImpl.invokeListeners(TaskContextImpl.scala:128)
	at org.apache.spark.TaskContextImpl.markTaskCompleted(TaskContextImpl.scala:116)
	at org.apache.spark.scheduler.Task.run(Task.scala:118)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
2019-09-07 17:40:29 WARN  NettyRpcEnv:66 - RpcEnv already stopped.
- score a single read covering a deletion
2019-09-07 17:40:38 WARN  TaskSetManager:66 - Stage 7 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- discover and force call hom alt deletion
2019-09-07 17:42:17 WARN  TaskSetManager:66 - Stage 7 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call hom alt AGCCAGTGGACGCCGACCT->A deletion at 1/875159
2019-09-07 17:44:10 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:44:20 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call hom alt TACACACACACACACACACACACACACACAC->T deletion at 1/1777263
2019-09-07 17:45:55 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:46:05 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call hom alt CAG->C deletion at 1/1067596
2019-09-07 17:48:16 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:48:23 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call hom alt C->G snp at 1/877715
2019-09-07 17:50:07 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:50:15 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call hom alt ACAG->A deletion at 1/886049
2019-09-07 17:52:00 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:52:07 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call hom alt GA->CC mnp at 1/889158–9
2019-09-07 17:53:42 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:53:50 WARN  TaskSetManager:66 - Stage 14 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call hom alt C->CCCCT insertion at 1/866511
2019-09-07 17:53:56 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:54:02 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call het ATG->A deletion at 1/905130
2019-09-07 17:55:44 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:55:51 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call het ATG->A deletion at 1/905130 while scoring all sites
2019-09-07 17:57:36 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:57:44 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call het AG->A deletion at 1/907170
2019-09-07 17:59:21 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 17:59:29 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call het T->G snp at 1/240898
2019-09-07 18:01:25 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 18:01:33 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- make het alt calls at biallelic snp locus
2019-09-07 18:03:45 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 18:03:55 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call hom alt T->TAAA insertion at 1/4120185
2019-09-07 18:06:16 WARN  BiallelicGenotyper:170 - Input RDD is not persisted. Performance may be degraded.
2019-09-07 18:06:23 WARN  TaskSetManager:66 - Stage 5 contains a task of very large size (10813 KB). The maximum recommended task size is 100 KB.
- call het alt TTATA,TTA->T insertion at 1/5274547
ObserverSuite:
- a fully clipped read will not generate any observations
- generate observations for a sequence match under diploid model
- generate observations for a read with an insertion under diploid model
- generate observations for a read with a deletion under diploid model
DiscoveredVariantSuite:
- round trip conversion to/from variant
SquareOffReferenceModelSuite:
- don't trim a snp
- trim a mnp
- trim an insertion
- don't trim a deletion
- extract variants finds sites with a called alt
- find genotype if variant is present
- don't find genotype if variant is not present
- excise a genotype from a reference block
- square off a site with data from multiple samples
DiscoverVariantsSuite:
- no variants in unaligned read
- no variants in rdd with unaligned read
- no variants in read that is a perfect sequence match
- no variants in rdd with sequence match reads
- find snp in read with a 1bp sequence mismatch
- find one snp in reads with 1bp sequence mismatch
- find insertion in read
- find insertion in reads
- find deletion in read
- find deletion in reads
- find variants in alignment record rdd
- break TT->CA mnp into two snps
ObservationOperatorSuite:
- zero operators are empty
- non-zero operators are non-empty
- cannot build mismatch with wrong ref length
- collapsing a non repeated set of operators should eliminate 0 ops
- collapsing a repeated set of operators with mixed match/mismatch
- collapse a set of operators with repeats
- collapse a set of operators with repeats and clips
- make a cigar and md tag from a single sequence match
- make a cigar and md tag from a single sequence mismatch
- make a cigar and md tag from a single multi-base sequence match
- make a cigar and md tag from a single deletion
- make a cigar and md tag from a single insertion
- make a cigar for a match followed by a deletion
- make a cigar for an insertion flanked by matches
- make a cigar for a match followed by a mismatch
- make a cigar for a multi-base mismatch flanked by matches
- make a cigar for a match after a clip
- make a cigar for a mismatch after a clip
- extract reference from a single snp
- extract reference from a single deletion
- extract reference from a single insertion
- extract reference from a soft clipped sequence
- extract reference from a hard clipped sequence
- extract reference from a match flanked deletion
- extract reference from a match flanked insertion
- read must be mapped to extract alignment operators
- extracting alignment operators will fail if cigar is unset
- extracting alignment operators will fail if cigar is *
- extracting alignment operators will fail if MD tag is unset
- extract alignment operators from a perfect read
- extract alignment operators from a read with a single mismatch
- extract alignment operators from a read with a single deletion
- extract alignment operators from a read with a single insertion
LogUtilsSuite:
- test our nifty log summer
- can we compute the sum of logs correctly?
- can we compute the additive inverse of logs correctly?
ObservationSuite:
- cannot create an observation with empty likelihoods
- cannot create an observation with 1-length likelihoods
- cannot create an observation with mismatching likelihood lengths
- forward strand must be >= 0
- forward strand cannot exceed coverage
- square map-q must be >= 0
- coverage is strictly positive
- invert an observation
- null an observation
RealignmentBlockSuite:
- folding over a clip returns the clip operator, soft clip
- folding over a clip returns the clip operator, hard clip
- folding over a canonical block returns the original alignment
- violate an invariant of the fold function, part 1
- violate an invariant of the fold function, part 2
- apply the fold function on a realignable block
- having a clip in the middle of a read is illegal
- can't have two soft clips back to back
- a read that is an exact sequence match is canonical
- hard clip before soft clip is ok at start of read
- hard clip after soft clip is ok at end of read
- a read with a single snp is canonical
- a read containing an indel with exact flanks is wholly realignable
- a read containing an indel with exact flanks is wholly realignable, with soft clipped bases
- a read containing an indel with longer flanks can be split into multiple blocks
- a read containing an indel with longer flanks on both sides can be split into multiple blocks
- properly handle a read that starts with a long soft clip
JointAnnotatorCallerSuite:
- discard reference site
- calculate MAF for all called genotypes
- calculate MAF ignoring uncalled genotypes
- roll up variant annotations from a single genotype
- roll up variant annotations across multiple genotypes
- recalling genotypes is a no-op for no calls and complex hets
- recall a genotype so that the state changes
- allele frequency being outside of (0.0, 1.0) just computes posteriors
- compute variant quality from a single genotype
- compute variant quality from multiple genotypes
CopyNumberMapSuite:
- create an empty map
- create a map with only diploid features
- create a map with a mix of features
PrefilterReadsSuite:
- filter on read uniqueness
- filter unmapped reads
- filter autosomal chromosomes with grc names
- filter sex chromosomes with grc names
- filter mitochondrial chromosome with a grc names
- filter autosomal chromosomes with hg names
- filter sex chromosomes with hg names
- filter mitochondrial chromosome with a hg names
- filter autosomal chromosomes from generator
- filter autosomal + sex chromosomes from generator
- filter all chromosomes from generator
- update a read whose mate is mapped to a filtered contig
- filter reads mapped to autosomal chromosomes from generator
- filter reads mapped to autosomal + sex chromosomes from generator
- filter reads mapped to all chromosomes from generator
- filter reads uniquely mapped to autosomal chromosomes from generator
- filter reads uniquely mapped to autosomal + sex chromosomes from generator
- filter reads uniquely mapped to all chromosomes from generator
- filter rdd of reads mapped to autosomal chromosomes from generator
- filter rdd of reads mapped to autosomal + sex chromosomes from generator
- filter rdd of reads mapped to all chromosomes from generator
- filter rdd of reads uniquely mapped to autosomal chromosomes from generator
- filter rdd of reads uniquely mapped to autosomal + sex chromosomes from generator
- filter rdd of reads uniquely mapped to all chromosomes from generator
Run completed in 33 minutes, 52 seconds.
Total number of tests run: 282
Suites: completed 23, aborted 0
Tests: succeeded 281, failed 1, canceled 0, ignored 1, pending 0
*** 1 TEST FAILED ***
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Skipping avocado: A Variant Caller, Distributed
[INFO] This project has been banned from the build due to previous failures.
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed ............. SUCCESS [  4.763 s]
[INFO] avocado-core: Core variant calling algorithms ...... FAILURE [34:30 min]
[INFO] avocado-cli: Command line interface for a distributed variant caller SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 34:35 min
[INFO] Finished at: 2019-09-07T18:08:26-07:00
[INFO] Final Memory: 32M/1156M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (test) on project avocado-core_2.11: There are test failures -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :avocado-core_2.11
Build step 'Execute shell' marked build as failure
Recording test results
ERROR: Step ‘Publish JUnit test result report’ failed: No test report files were found. Configuration error?
Sending e-mails to: fnothaft@berkeley.edu
Finished: FAILURE