FailedConsole Output

Skipping 1,425 KB.. Full Log
QUlDDI2RQXJOYpFJdU5qTaKoEttlJQdnYxAAJrJTsAN/bC9aUAAAA=  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)
2019-10-07 00:10:30 ERROR SparkContext:91 - Error initializing SparkContext.
java.lang.IllegalStateException: Shutdown hooks cannot be modified during shutdown.
	at org.apache.spark.util.SparkShutdownHookManager.add(ShutdownHookManager.scala:195)
	at org.apache.spark.util.ShutdownHookManager$.addShutdownHook(ShutdownHookManager.scala:153)
	at org.apache.spark.storage.DiskBlockManager.addShutdownHook(DiskBlockManager.scala:145)
	at org.apache.spark.storage.DiskBlockManager.<init>(DiskBlockManager.scala:51)
	at org.apache.spark.storage.BlockManager.<init>(BlockManager.scala:131)
	at org.apache.spark.SparkEnv$.create(SparkEnv.scala:351)
	at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:175)
	at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:257)
	at org.apache.spark.SparkContext.<init>(SparkContext.scala:432)
	at org.bdgenomics.utils.misc.SparkFunSuite$class.setupSparkContext(SparkFunSuite.scala:56)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.setupSparkContext(PrefilterReadsSuite.scala:37)
	at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:99)
	at org.bdgenomics.utils.misc.SparkFunSuite$$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$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
	at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
	at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$runTest(PrefilterReadsSuite.scala:37)
	at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.runTest(PrefilterReadsSuite.scala:37)
	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.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$run(PrefilterReadsSuite.scala:37)
	at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.run(PrefilterReadsSuite.scala:37)
	at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
	at org.scalatest.Suite$$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$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
	at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
	at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
	at org.scalatest.tools.Runner$.main(Runner.scala:860)
	at org.scalatest.tools.Runner.main(Runner.scala)
- filter rdd of reads uniquely mapped to autosomal chromosomes from generator *** FAILED ***
  java.lang.IllegalStateException: Shutdown hooks cannot be modified during shutdown.
  at org.apache.spark.util.SparkShutdownHookManager.add(ShutdownHookManager.scala:195)
  at org.apache.spark.util.ShutdownHookManager$.addShutdownHook(ShutdownHookManager.scala:153)
  at org.apache.spark.storage.DiskBlockManager.addShutdownHook(DiskBlockManager.scala:145)
  at org.apache.spark.storage.DiskBlockManager.<init>(DiskBlockManager.scala:51)
  at org.apache.spark.storage.BlockManager.<init>(BlockManager.scala:131)
  at org.apache.spark.SparkEnv$.create(SparkEnv.scala:351)
  at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:175)
  at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:257)
  at org.apache.spark.SparkContext.<init>(SparkContext.scala:432)
  at org.bdgenomics.utils.misc.SparkFunSuite$class.setupSparkContext(SparkFunSuite.scala:56)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.setupSparkContext(PrefilterReadsSuite.scala:37)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:99)
  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)
2019-10-07 00:10:30 WARN  SparkContext:66 - Another SparkContext is being constructed (or threw an exception in its constructor).  This may indicate an error, since only one SparkContext may be running in this JVM (see SPARK-2243). The other SparkContext was created at:
  at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
  at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
org.apache.spark.SparkContext.<init>(SparkContext.scala:76)
org.bdgenomics.utils.misc.SparkFunSuite$class.setupSparkContext(SparkFunSuite.scala:56)
org.bdgenomics.avocado.util.PrefilterReadsSuite.setupSparkContext(PrefilterReadsSuite.scala:37)
org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:99)
org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
  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)
org.scalatest.Transformer.apply(Transformer.scala:22)
org.scalatest.Transformer.apply(Transformer.scala:20)
org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
org.scalatest.Suite$class.withFixture(Suite.scala:1122)
org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$runTest(PrefilterReadsSuite.scala:37)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$runTest(PrefilterReadsSuite.scala:37)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.runTest(PrefilterReadsSuite.scala:37)
  at org.scalatest.FunSuiteLike$$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$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$run(PrefilterReadsSuite.scala:37)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.run(PrefilterReadsSuite.scala:37)
  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)
2019-10-07 00:10:30 ERROR SparkContext:91 - Error initializing SparkContext.
java.lang.IllegalStateException: Shutdown hooks cannot be modified during shutdown.
	at org.apache.spark.util.SparkShutdownHookManager.add(ShutdownHookManager.scala:195)
	at org.apache.spark.util.ShutdownHookManager$.addShutdownHook(ShutdownHookManager.scala:153)
	at org.apache.spark.storage.DiskBlockManager.addShutdownHook(DiskBlockManager.scala:145)
	at org.apache.spark.storage.DiskBlockManager.<init>(DiskBlockManager.scala:51)
	at org.apache.spark.storage.BlockManager.<init>(BlockManager.scala:131)
	at org.apache.spark.SparkEnv$.create(SparkEnv.scala:351)
	at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:175)
	at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:257)
	at org.apache.spark.SparkContext.<init>(SparkContext.scala:432)
	at org.bdgenomics.utils.misc.SparkFunSuite$class.setupSparkContext(SparkFunSuite.scala:56)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.setupSparkContext(PrefilterReadsSuite.scala:37)
	at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:99)
	at org.bdgenomics.utils.misc.SparkFunSuite$$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$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
	at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
	at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$runTest(PrefilterReadsSuite.scala:37)
	at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.runTest(PrefilterReadsSuite.scala:37)
	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.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$run(PrefilterReadsSuite.scala:37)
	at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.run(PrefilterReadsSuite.scala:37)
	at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
	at org.scalatest.Suite$$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$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
	at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
	at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
	at org.scalatest.tools.Runner$.main(Runner.scala:860)
	at org.scalatest.tools.Runner.main(Runner.scala)
- filter rdd of reads uniquely mapped to autosomal + sex chromosomes from generator *** FAILED ***
  java.lang.IllegalStateException: Shutdown hooks cannot be modified during shutdown.
  at org.apache.spark.util.SparkShutdownHookManager.add(ShutdownHookManager.scala:195)
2019-10-07 00:10:30 WARN  SparkContext:66 - Another SparkContext is being constructed (or threw an exception in its constructor).  This may indicate an error, since only one SparkContext may be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:76)
org.bdgenomics.utils.misc.SparkFunSuite$class.setupSparkContext(SparkFunSuite.scala:56)
org.bdgenomics.avocado.util.PrefilterReadsSuite.setupSparkContext(PrefilterReadsSuite.scala:37)
org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:99)
org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
  at org.apache.spark.util.ShutdownHookManager$.addShutdownHook(ShutdownHookManager.scala:153)
  at org.apache.spark.storage.DiskBlockManager.addShutdownHook(DiskBlockManager.scala:145)
  at org.apache.spark.storage.DiskBlockManager.<init>(DiskBlockManager.scala:51)
  at org.apache.spark.storage.BlockManager.<init>(BlockManager.scala:131)
  at org.apache.spark.SparkEnv$.create(SparkEnv.scala:351)
  at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:175)
  at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:257)
org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
  at org.apache.spark.SparkContext.<init>(SparkContext.scala:432)
  at org.bdgenomics.utils.misc.SparkFunSuite$class.setupSparkContext(SparkFunSuite.scala:56)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.setupSparkContext(PrefilterReadsSuite.scala:37)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:99)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
  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)
org.scalatest.Transformer.apply(Transformer.scala:22)
org.scalatest.Transformer.apply(Transformer.scala:20)
org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
org.scalatest.Suite$class.withFixture(Suite.scala:1122)
org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$runTest(PrefilterReadsSuite.scala:37)
  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.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$runTest(PrefilterReadsSuite.scala:37)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.runTest(PrefilterReadsSuite.scala:37)
  at org.scalatest.FunSuiteLike$$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$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$run(PrefilterReadsSuite.scala:37)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.run(PrefilterReadsSuite.scala:37)
  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)
2019-10-07 00:10:30 ERROR SparkContext:91 - Error initializing SparkContext.
java.lang.IllegalStateException: Shutdown hooks cannot be modified during shutdown.
	at org.apache.spark.util.SparkShutdownHookManager.add(ShutdownHookManager.scala:195)
	at org.apache.spark.util.ShutdownHookManager$.addShutdownHook(ShutdownHookManager.scala:153)
	at org.apache.spark.storage.DiskBlockManager.addShutdownHook(DiskBlockManager.scala:145)
	at org.apache.spark.storage.DiskBlockManager.<init>(DiskBlockManager.scala:51)
	at org.apache.spark.storage.BlockManager.<init>(BlockManager.scala:131)
	at org.apache.spark.SparkEnv$.create(SparkEnv.scala:351)
	at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:175)
	at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:257)
	at org.apache.spark.SparkContext.<init>(SparkContext.scala:432)
	at org.bdgenomics.utils.misc.SparkFunSuite$class.setupSparkContext(SparkFunSuite.scala:56)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.setupSparkContext(PrefilterReadsSuite.scala:37)
	at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:99)
	at org.bdgenomics.utils.misc.SparkFunSuite$$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$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
	at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
	at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$runTest(PrefilterReadsSuite.scala:37)
	at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.runTest(PrefilterReadsSuite.scala:37)
	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.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$run(PrefilterReadsSuite.scala:37)
	at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
	at org.bdgenomics.avocado.util.PrefilterReadsSuite.run(PrefilterReadsSuite.scala:37)
	at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
	at org.scalatest.Suite$$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$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
	at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
	at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
	at org.scalatest.tools.Runner$.main(Runner.scala:860)
	at org.scalatest.tools.Runner.main(Runner.scala)
- filter rdd of reads uniquely mapped to all chromosomes from generator *** FAILED ***
  java.lang.IllegalStateException: Shutdown hooks cannot be modified during shutdown.
  at org.apache.spark.util.SparkShutdownHookManager.add(ShutdownHookManager.scala:195)
  at org.apache.spark.util.ShutdownHookManager$.addShutdownHook(ShutdownHookManager.scala:153)
  at org.apache.spark.storage.DiskBlockManager.addShutdownHook(DiskBlockManager.scala:145)
  at org.apache.spark.storage.DiskBlockManager.<init>(DiskBlockManager.scala:51)
  at org.apache.spark.storage.BlockManager.<init>(BlockManager.scala:131)
  at org.apache.spark.SparkEnv$.create(SparkEnv.scala:351)
  at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:175)
  at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:257)
  at org.apache.spark.SparkContext.<init>(SparkContext.scala:432)
  at org.bdgenomics.utils.misc.SparkFunSuite$class.setupSparkContext(SparkFunSuite.scala:56)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.setupSparkContext(PrefilterReadsSuite.scala:37)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:99)
  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.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$runTest(PrefilterReadsSuite.scala:37)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.runTest(PrefilterReadsSuite.scala:37)
  at org.scalatest.FunSuiteLike$$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$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$super$run(PrefilterReadsSuite.scala:37)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.run(PrefilterReadsSuite.scala:37)
  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)
Run completed in 10 minutes, 5 seconds.
Total number of tests run: 282
Suites: completed 23, aborted 0
Tests: succeeded 251, failed 31, canceled 0, ignored 1, pending 0
*** 31 TESTS FAILED ***
2019-10-07 00:12:21 ERROR ContextCleaner:91 - Error cleaning broadcast 8
org.apache.spark.rpc.RpcTimeoutException: Cannot receive any reply from 192.168.10.32:55910 in 120 seconds. This timeout is controlled by spark.rpc.askTimeout
	at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:47)
	at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:62)
	at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:58)
	at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
	at scala.util.Failure$$anonfun$recover$1.apply(Try.scala:215)
	at scala.util.Try$.apply(Try.scala:191)
	at scala.util.Failure.recover(Try.scala:215)
	at scala.concurrent.Future$$anonfun$recover$1.apply(Future.scala:324)
	at scala.concurrent.Future$$anonfun$recover$1.apply(Future.scala:324)
	at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)
	at org.spark_project.guava.util.concurrent.MoreExecutors$SameThreadExecutorService.execute(MoreExecutors.java:293)
	at scala.concurrent.impl.ExecutionContextImpl$$anon$1.execute(ExecutionContextImpl.scala:136)
	at scala.concurrent.impl.CallbackRunnable.executeWithValue(Promise.scala:40)
	at scala.concurrent.impl.Promise$DefaultPromise.tryComplete(Promise.scala:248)
	at scala.concurrent.Promise$class.complete(Promise.scala:55)
	at scala.concurrent.impl.Promise$DefaultPromise.complete(Promise.scala:153)
	at scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:235)
	at scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:235)
	at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)
	at scala.concurrent.BatchingExecutor$Batch$$anonfun$run$1.processBatch$1(BatchingExecutor.scala:63)
	at scala.concurrent.BatchingExecutor$Batch$$anonfun$run$1.apply$mcV$sp(BatchingExecutor.scala:78)
	at scala.concurrent.BatchingExecutor$Batch$$anonfun$run$1.apply(BatchingExecutor.scala:55)
	at scala.concurrent.BatchingExecutor$Batch$$anonfun$run$1.apply(BatchingExecutor.scala:55)
	at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:72)
	at scala.concurrent.BatchingExecutor$Batch.run(BatchingExecutor.scala:54)
	at scala.concurrent.Future$InternalCallbackExecutor$.unbatchedExecute(Future.scala:599)
	at scala.concurrent.BatchingExecutor$class.execute(BatchingExecutor.scala:106)
	at scala.concurrent.Future$InternalCallbackExecutor$.execute(Future.scala:597)
	at scala.concurrent.impl.CallbackRunnable.executeWithValue(Promise.scala:40)
	at scala.concurrent.impl.Promise$DefaultPromise.tryComplete(Promise.scala:248)
	at scala.concurrent.Promise$class.tryFailure(Promise.scala:115)
	at scala.concurrent.impl.Promise$DefaultPromise.tryFailure(Promise.scala:153)
	at org.apache.spark.rpc.netty.NettyRpcEnv.org$apache$spark$rpc$netty$NettyRpcEnv$$onFailure$1(NettyRpcEnv.scala:205)
	at org.apache.spark.rpc.netty.NettyRpcEnv$$anon$1.run(NettyRpcEnv.scala:239)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.TimeoutException: Cannot receive any reply from 192.168.10.32:55910 in 120 seconds
	... 8 more
2019-10-07 00:12:21 WARN  BlockManagerMaster:87 - Failed to remove broadcast 8 with removeFromMaster = true - Cannot receive any reply from 192.168.10.32:55910 in 120 seconds. This timeout is controlled by spark.rpc.askTimeout
org.apache.spark.rpc.RpcTimeoutException: Cannot receive any reply from 192.168.10.32:55910 in 120 seconds. This timeout is controlled by spark.rpc.askTimeout
	at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:47)
	at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:62)
	at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:58)
	at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
	at scala.util.Failure$$anonfun$recover$1.apply(Try.scala:215)
	at scala.util.Try$.apply(Try.scala:191)
	at scala.util.Failure.recover(Try.scala:215)
	at scala.concurrent.Future$$anonfun$recover$1.apply(Future.scala:324)
	at scala.concurrent.Future$$anonfun$recover$1.apply(Future.scala:324)
	at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)
	at org.spark_project.guava.util.concurrent.MoreExecutors$SameThreadExecutorService.execute(MoreExecutors.java:293)
	at scala.concurrent.impl.ExecutionContextImpl$$anon$1.execute(ExecutionContextImpl.scala:136)
	at scala.concurrent.impl.CallbackRunnable.executeWithValue(Promise.scala:40)
	at scala.concurrent.impl.Promise$DefaultPromise.tryComplete(Promise.scala:248)
	at scala.concurrent.Promise$class.complete(Promise.scala:55)
	at scala.concurrent.impl.Promise$DefaultPromise.complete(Promise.scala:153)
	at scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:235)
	at scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:235)
	at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)
	at scala.concurrent.BatchingExecutor$Batch$$anonfun$run$1.processBatch$1(BatchingExecutor.scala:63)
	at scala.concurrent.BatchingExecutor$Batch$$anonfun$run$1.apply$mcV$sp(BatchingExecutor.scala:78)
	at scala.concurrent.BatchingExecutor$Batch$$anonfun$run$1.apply(BatchingExecutor.scala:55)
	at scala.concurrent.BatchingExecutor$Batch$$anonfun$run$1.apply(BatchingExecutor.scala:55)
	at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:72)
	at scala.concurrent.BatchingExecutor$Batch.run(BatchingExecutor.scala:54)
	at scala.concurrent.Future$InternalCallbackExecutor$.unbatchedExecute(Future.scala:599)
	at scala.concurrent.BatchingExecutor$class.execute(BatchingExecutor.scala:106)
	at scala.concurrent.Future$InternalCallbackExecutor$.execute(Future.scala:597)
	at scala.concurrent.impl.CallbackRunnable.executeWithValue(Promise.scala:40)
	at scala.concurrent.impl.Promise$DefaultPromise.tryComplete(Promise.scala:248)
	at scala.concurrent.Promise$class.tryFailure(Promise.scala:115)
	at scala.concurrent.impl.Promise$DefaultPromise.tryFailure(Promise.scala:153)
	at org.apache.spark.rpc.netty.NettyRpcEnv.org$apache$spark$rpc$netty$NettyRpcEnv$$onFailure$1(NettyRpcEnv.scala:205)
	at org.apache.spark.rpc.netty.NettyRpcEnv$$anon$1.run(NettyRpcEnv.scala:239)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
	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)
Caused by: java.util.concurrent.TimeoutException: Cannot receive any reply from 192.168.10.32:55910 in 120 seconds
	... 8 more
[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 [  4.270 s]
[INFO] avocado-core: Core variant calling algorithms ...... FAILURE [12:30 min]
[INFO] avocado-cli: Command line interface for a distributed variant caller SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 12:35 min
[INFO] Finished at: 2019-10-07T00:12:21-07:00
[INFO] Final Memory: 34M/1155M
[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