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)