Failed

org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.call hom alt T->TAAA insertion at 1/4120185

Failing for the past 1 build (Since #237 )

Error Message

java.lang.reflect.InvocationTargetException was thrown.

Stacktrace

      java.lang.reflect.InvocationTargetException
      at sun.reflect.GeneratedMethodAccessor66.invoke(Unknown Source)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.bdgenomics.utils.misc.HadoopUtil$.newJob(HadoopUtil.scala:35)
      at org.bdgenomics.utils.misc.HadoopUtil$.newJob(HadoopUtil.scala:48)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1.apply(ADAMContext.scala:1564)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1.apply(ADAMContext.scala:1522)
      at scala.Option.fold(Option.scala:158)
      at org.apache.spark.rdd.Timer.time(Timer.scala:48)
      at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1522)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:3280)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:3271)
      at scala.Option.fold(Option.scala:158)
      at org.apache.spark.rdd.Timer.time(Timer.scala:48)
      at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3271)
      at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$38.apply$mcV$sp(BiallelicGenotyperSuite.scala:867)
      at org.bdgenomics.utils.misc.SparkFunSuite$$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.NoClassDefFoundError: Could not initialize class org.apache.hadoop.security.Credentials
      at org.apache.hadoop.mapred.JobConf.<init>(JobConf.java:334)
      at org.apache.hadoop.mapreduce.Job.getInstance(Job.java:184)
      at sun.reflect.GeneratedMethodAccessor66.invoke(Unknown Source)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.bdgenomics.utils.misc.HadoopUtil$.newJob(HadoopUtil.scala:35)
      at org.bdgenomics.utils.misc.HadoopUtil$.newJob(HadoopUtil.scala:48)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1.apply(ADAMContext.scala:1564)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1.apply(ADAMContext.scala:1522)
      at scala.Option.fold(Option.scala:158)
      at org.apache.spark.rdd.Timer.time(Timer.scala:48)
      at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1522)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:3280)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:3271)
      at scala.Option.fold(Option.scala:158)
      at org.apache.spark.rdd.Timer.time(Timer.scala:48)
      at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3271)
      at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$38.apply$mcV$sp(BiallelicGenotyperSuite.scala:867)
      at org.bdgenomics.utils.misc.SparkFunSuite$$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)