Class org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark > BaseRecalibratorSparkIntegrationTest

tests

failures

ignored

2.671s

duration

successful

Failed tests
Tests
Standard output
Standard error

Failed tests

testBQSRSpark[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@199e8d7f)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@57816e8d)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@6ab85f31)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@44e85437)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@4c328b47)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[10](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@5c96da5e)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@348feab)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@5cecfba1)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@b4b86e2)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@6e275cd7)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[1](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@3f97d840)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@52a4d953)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@20e02ed2)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@70a415e3)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@7155af41)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@75cd91c6)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@3ef0cf06)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@a3e9fa)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@2f84745e)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@7a68dfc9)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args=''))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@56f20b06)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@4d18d074)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@61faffa3)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@15861ec8)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@a736515)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[4](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --indels-context-size 4'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@3d42ea42)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@27d7c8a)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@25427f99)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@5b58ebf6)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@2f1d147e)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[5](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --low-quality-tail 5'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@c33c7d4)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@5ae2f56b)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@1e62f5a7)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@51e4d5ea)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@6eec7428)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[6](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --quantizing-levels 6'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@3e885f0d)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@313fd177)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@79cb52d9)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@2972298)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@386068f3)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[7](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --mismatches-context-size 4'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@4ec94597)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@12be5077)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@7ccae1af)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@3ee40396)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@3717d34c)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.bam', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@44ce3c1c)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@38416669)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@79e5748b)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@701df34b)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@503c4eec)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

testBQSRSpark[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf'))

java.lang.RuntimeException: org.apache.spark.SparkException: Task not serializable
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:213)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:180)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
	at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
	at org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest.testBQSRSpark(BaseRecalibratorSparkIntegrationTest.java:111)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.apache.spark.SparkException: Task not serializable
	at app//org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:444)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:416)
	at app//org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:163)
	at app//org.apache.spark.SparkContext.clean(SparkContext.scala:2674)
	at app//org.apache.spark.rdd.RDD.$anonfun$mapPartitions$1(RDD.scala:852)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:851)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$2(RDD.scala:1262)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1253)
	at app//org.apache.spark.rdd.RDD.$anonfun$treeAggregate$1(RDD.scala:1239)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at app//org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at app//org.apache.spark.rdd.RDD.withScope(RDD.scala:407)
	at app//org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1239)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate(JavaRDDLike.scala:440)
	at app//org.apache.spark.api.java.JavaRDDLike.treeAggregate$(JavaRDDLike.scala:435)
	at app//org.apache.spark.api.java.AbstractJavaRDDLike.treeAggregate(JavaRDDLike.scala:45)
	at app//org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.apply(BaseRecalibratorSparkFn.java:42)
	at app//org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.runTool(BaseRecalibratorSpark.java:132)
	at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:535)
	at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:208)
	... 50 more
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@3b6c604e)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, name: reflections, type: class org.reflections.Reflections)
	- object (class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList, org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList@2ca7b5cb)
	- field (class: org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, name: covariates, type: class org.broadinstitute.hellbender.utils.recalibration.covariates.BQSRCovariateList)
	- object (class org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables, org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables@80af82e)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 3)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$4:(Ljava/lang/Object;Lscala/Function2;Lscala/Function2;Lscala/collection/Iterator;)Ljava/lang/Object;, instantiatedMethodType=(Lscala/collection/Iterator;)Ljava/lang/Object;, numCaptured=3])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548, org.apache.spark.rdd.RDD$$Lambda$2653/0x00007fa779046548@10bdb0e0)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$anonfun$treeAggregate$6:(Lscala/Function1;Lscala/collection/Iterator;)Lscala/collection/Iterator;, instantiatedMethodType=(Lscala/collection/Iterator;)Lscala/collection/Iterator;, numCaptured=1])
	- writeReplace data (class: java.lang.invoke.SerializedLambda)
	- object (class org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918, org.apache.spark.rdd.RDD$$Lambda$2654/0x00007fa779046918@4d44a1f6)
	at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:41)
	at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:49)
	at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:115)
	at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:441)
	... 84 more

Tests

Test	Duration	Result
testBQSRSpark[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq'))	0.260s	failed
testBQSRSpark[10](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf'))	0.259s	failed
testBQSRSpark[1](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq'))	0.301s	failed
testBQSRSpark[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq'))	0.303s	failed
testBQSRSpark[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args=''))	0.225s	failed
testBQSRSpark[4](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --indels-context-size 4'))	0.211s	failed
testBQSRSpark[5](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --low-quality-tail 5'))	0.240s	failed
testBQSRSpark[6](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --quantizing-levels 6'))	0.222s	failed
testBQSRSpark[7](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --mismatches-context-size 4'))	0.207s	failed
testBQSRSpark[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.bam', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf'))	0.248s	failed
testBQSRSpark[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf'))	0.195s	failed

Standard output

--------------------------------------------------------------------------------
[20:58:20] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[20:58:20] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[20:58:20] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq
--------------------------------------------------------------------------------
[20:58:21] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark-
--------------------------------------------------------------------------------
[20:58:21] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --indels-context-size 4
--------------------------------------------------------------------------------
[20:58:21] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --low-quality-tail 5
--------------------------------------------------------------------------------
[20:58:21] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --quantizing-levels 6
--------------------------------------------------------------------------------
[20:58:21] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --mismatches-context-size 4
--------------------------------------------------------------------------------
[20:58:22] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf
--------------------------------------------------------------------------------
[20:58:22] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_138.b37.21.10m-10m100.vcf
--------------------------------------------------------------------------------
[20:58:22] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSpark--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf

Standard error

[June 12, 2025 at 8:58:20 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:20 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:21 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:21 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:21 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:21 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:21 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:22 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:22 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:22 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280
[June 12, 2025 at 8:58:22 PM GMT] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3177185280