FailedConsole Output

Skipping 880 KB.. Full Log
P3gkqLMvHTriiIGKaihyfl5xfk5qXrOEBpkDgMEMDIxMFQUlDCw2+gXFyTm2QEAI9P8iI4AAAA=
  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$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
- filter rdd of reads uniquely mapped to autosomal chromosomes from generator *** FAILED ***
  java.io.IOException: Class not found
  at org.apache.xbean.asm5.ClassReader.a(Unknown Source)
  at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
  at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:42)
  at org.apache.spark.util.ClosureCleaner$.getInnerClosureClasses(ClosureCleaner.scala:83)
  at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:173)
  at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:108)
  at org.apache.spark.SparkContext.clean(SparkContext.scala:2287)
  at org.apache.spark.rdd.RDD$$anonfun$filter$1.apply(RDD.scala:387)
  at org.apache.spark.rdd.RDD$$anonfun$filter$1.apply(RDD.scala:386)
  at org.apache.spark.rdd.RDDOperationScope$.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.filter(RDD.scala:386)
  at org.bdgenomics.avocado.util.PrefilterReads$$anonfun$apply$1.apply(PrefilterReads.scala:81)
  at org.bdgenomics.avocado.util.PrefilterReads$$anonfun$apply$1.apply(PrefilterReads.scala:80)
  at org.bdgenomics.adam.rdd.GenomicDataset$class.transform(GenomicRDD.scala:450)
  at org.bdgenomics.adam.rdd.AvroGenomicDataset.transform(GenomicRDD.scala:3712)
  at org.bdgenomics.avocado.util.PrefilterReads$.apply(PrefilterReads.scala:80)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.testRdd(PrefilterReadsSuite.scala:212)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite$$anonfun$22.apply$mcV$sp(PrefilterReadsSuite.scala:231)
  at org.bdgenomics.utils.misc.SparkFunSuite$$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.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.io.IOException: Class not found
  at org.apache.xbean.asm5.ClassReader.a(Unknown Source)
  at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
  at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:42)
  at org.apache.spark.util.ClosureCleaner$.getInnerClosureClasses(ClosureCleaner.scala:83)
  at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:173)
  at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:108)
  at org.apache.spark.SparkContext.clean(SparkContext.scala:2287)
  at org.apache.spark.rdd.RDD$$anonfun$filter$1.apply(RDD.scala:387)
  at org.apache.spark.rdd.RDD$$anonfun$filter$1.apply(RDD.scala:386)
  at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
  at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
  at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
  at org.apache.spark.rdd.RDD.filter(RDD.scala:386)
  at org.bdgenomics.avocado.util.PrefilterReads$$anonfun$apply$1.apply(PrefilterReads.scala:81)
  at org.bdgenomics.avocado.util.PrefilterReads$$anonfun$apply$1.apply(PrefilterReads.scala:80)
  at org.bdgenomics.adam.rdd.GenomicDataset$class.transform(GenomicRDD.scala:450)
  at org.bdgenomics.adam.rdd.AvroGenomicDataset.transform(GenomicRDD.scala:3712)
  at org.bdgenomics.avocado.util.PrefilterReads$.apply(PrefilterReads.scala:80)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.testRdd(PrefilterReadsSuite.scala:212)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite$$anonfun$23.apply$mcV$sp(PrefilterReadsSuite.scala:236)
  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$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.org$scalatest$BeforeAndAfter$$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$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
- filter rdd of reads uniquely mapped to all chromosomes from generator *** FAILED ***
  java.io.IOException: Class not found
  at org.apache.xbean.asm5.ClassReader.a(Unknown Source)
  at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
  at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:42)
  at org.apache.spark.util.ClosureCleaner$.getInnerClosureClasses(ClosureCleaner.scala:83)
  at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:173)
  at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:108)
  at org.apache.spark.SparkContext.clean(SparkContext.scala:2287)
  at org.apache.spark.rdd.RDD$$anonfun$filter$1.apply(RDD.scala:387)
  at org.apache.spark.rdd.RDD$$anonfun$filter$1.apply(RDD.scala:386)
  at org.apache.spark.rdd.RDDOperationScope$.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.filter(RDD.scala:386)
  at org.bdgenomics.avocado.util.PrefilterReads$$anonfun$apply$1.apply(PrefilterReads.scala:81)
  at org.bdgenomics.avocado.util.PrefilterReads$$anonfun$apply$1.apply(PrefilterReads.scala:80)
  at org.bdgenomics.adam.rdd.GenomicDataset$class.transform(GenomicRDD.scala:450)
  at org.bdgenomics.adam.rdd.AvroGenomicDataset.transform(GenomicRDD.scala:3712)
  at org.bdgenomics.avocado.util.PrefilterReads$.apply(PrefilterReads.scala:80)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite.testRdd(PrefilterReadsSuite.scala:212)
  at org.bdgenomics.avocado.util.PrefilterReadsSuite$$anonfun$24.apply$mcV$sp(PrefilterReadsSuite.scala:241)
  at org.bdgenomics.utils.misc.SparkFunSuite$$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.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)
Reporter completed abruptly with an exception after receiving event: SuiteCompleted(Ordinal(1, 612),PrefilterReadsSuite,org.bdgenomics.avocado.util.PrefilterReadsSuite,Some(org.bdgenomics.avocado.util.PrefilterReadsSuite),Some(284),Some(MotionToSuppress),Some(TopOfClass(org.bdgenomics.avocado.util.PrefilterReadsSuite)),Some(org.bdgenomics.avocado.util.PrefilterReadsSuite),None,ScalaTest-main-running-DiscoverySuite,1557562813076).
java.io.FileNotFoundException: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/scalatest-reports/./TEST-org.bdgenomics.avocado.util.PrefilterReadsSuite.xml (No such file or directory)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(FileOutputStream.java:270)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:162)
	at java.io.PrintWriter.<init>(PrintWriter.java:192)
	at java.io.PrintWriter.<init>(PrintWriter.java:232)
	at org.scalatest.tools.JUnitXmlReporter.writeSuiteFile(JUnitXmlReporter.scala:80)
	at org.scalatest.tools.JUnitXmlReporter.apply(JUnitXmlReporter.scala:59)
	at org.scalatest.DispatchReporter$Propagator$$anonfun$run$1.apply(DispatchReporter.scala:240)
	at org.scalatest.DispatchReporter$Propagator$$anonfun$run$1.apply(DispatchReporter.scala:239)
	at scala.collection.immutable.List.foreach(List.scala:381)
	at org.scalatest.DispatchReporter$Propagator.run(DispatchReporter.scala:239)
	at java.lang.Thread.run(Thread.java:748)
Reporter completed abruptly with an exception after receiving event: SuiteCompleted(Ordinal(1, 613),DiscoverySuite,org.scalatest.tools.DiscoverySuite-9409b74b-e459-48fe-8d6a-d828a214aa9c,Some(org.scalatest.tools.DiscoverySuite),Some(920048),Some(MotionToSuppress),Some(TopOfClass(org.scalatest.tools.DiscoverySuite)),None,None,ScalaTest-main,1557562813078).
java.io.FileNotFoundException: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.2.0/label/ubuntu/avocado-core/target/scalatest-reports/./TEST-org.scalatest.tools.DiscoverySuite-9409b74b-e459-48fe-8d6a-d828a214aa9c.xml (No such file or directory)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(FileOutputStream.java:270)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:162)
	at java.io.PrintWriter.<init>(PrintWriter.java:192)
	at java.io.PrintWriter.<init>(PrintWriter.java:232)
	at org.scalatest.tools.JUnitXmlReporter.writeSuiteFile(JUnitXmlReporter.scala:80)
	at org.scalatest.tools.JUnitXmlReporter.apply(JUnitXmlReporter.scala:59)
	at org.scalatest.DispatchReporter$Propagator$$anonfun$run$1.apply(DispatchReporter.scala:240)
	at org.scalatest.DispatchReporter$Propagator$$anonfun$run$1.apply(DispatchReporter.scala:239)
	at scala.collection.immutable.List.foreach(List.scala:381)
	at org.scalatest.DispatchReporter$Propagator.run(DispatchReporter.scala:239)
	at java.lang.Thread.run(Thread.java:748)
Run completed in 15 minutes, 20 seconds.
Total number of tests run: 282
Suites: completed 23, aborted 0
Tests: succeeded 259, failed 23, canceled 0, ignored 1, pending 0
*** 23 TESTS 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 [  4.452 s]
[INFO] avocado-core: Core variant calling algorithms ...... FAILURE [15:56 min]
[INFO] avocado-cli: Command line interface for a distributed variant caller SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 16:01 min
[INFO] Finished at: 2019-05-11T01:20:13-07:00
[INFO] Final Memory: 34M/1110M
[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