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

all > org.broadinstitute.hellbender.tools.spark > BaseRecalibratorSparkIntegrationTest
9

tests
7

failures
0

ignored
10.132s

duration
22%

successful

Failed tests

testBQSRSparkCloud[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.testBQSRSparkCloud(BaseRecalibratorSparkIntegrationTest.java:148)
	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:568)
	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:568)
	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@46b4d4e7)
	- 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@1d8cfad5)
	- 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@74cf108b)
	- 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$$Lambda$2185/0x0000000801a36a48, org.apache.spark.rdd.RDD$$Lambda$2185/0x0000000801a36a48@749330a8)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2186/0x0000000801a36e18, org.apache.spark.rdd.RDD$$Lambda$2186/0x0000000801a36e18@4b7272d6)
	at org.apache.spark.serializer.SerializationDebugger$.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

testBQSRSparkCloud[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.testBQSRSparkCloud(BaseRecalibratorSparkIntegrationTest.java:148)
	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:568)
	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:568)
	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@20c642ef)
	- 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@78e5b18)
	- 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@6fcd767a)
	- 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$$Lambda$2185/0x0000000801a36a48, org.apache.spark.rdd.RDD$$Lambda$2185/0x0000000801a36a48@6e3f38c1)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2186/0x0000000801a36e18, org.apache.spark.rdd.RDD$$Lambda$2186/0x0000000801a36e18@3564caf8)
	at org.apache.spark.serializer.SerializationDebugger$.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

testBQSRSparkCloud[2](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.testBQSRSparkCloud(BaseRecalibratorSparkIntegrationTest.java:148)
	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:568)
	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:568)
	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@17e71422)
	- 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@60df0131)
	- 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@ce4a8a2)
	- 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$$Lambda$2185/0x0000000801a36a48, org.apache.spark.rdd.RDD$$Lambda$2185/0x0000000801a36a48@43139322)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2186/0x0000000801a36e18, org.apache.spark.rdd.RDD$$Lambda$2186/0x0000000801a36e18@41576e84)
	at org.apache.spark.serializer.SerializationDebugger$.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

testBQSRSparkCloud[3](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.testBQSRSparkCloud(BaseRecalibratorSparkIntegrationTest.java:148)
	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:568)
	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:568)
	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@3e6be3c1)
	- 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@68b2ce71)
	- 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@3a5c472)
	- 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$$Lambda$2185/0x0000000801a36a48, org.apache.spark.rdd.RDD$$Lambda$2185/0x0000000801a36a48@1b54ae72)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2186/0x0000000801a36e18, org.apache.spark.rdd.RDD$$Lambda$2186/0x0000000801a36e18@30350c73)
	at org.apache.spark.serializer.SerializationDebugger$.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

testBQSRSparkCloud[4](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.testBQSRSparkCloud(BaseRecalibratorSparkIntegrationTest.java:148)
	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:568)
	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:568)
	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@2cdb1581)
	- 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@3d640f70)
	- 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@35a6f370)
	- 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$$Lambda$2185/0x0000000801a36a48, org.apache.spark.rdd.RDD$$Lambda$2185/0x0000000801a36a48@3b977a31)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2186/0x0000000801a36e18, org.apache.spark.rdd.RDD$$Lambda$2186/0x0000000801a36e18@5eab3eac)
	at org.apache.spark.serializer.SerializationDebugger$.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

testBQSRSparkCloud[5](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.testBQSRSparkCloud(BaseRecalibratorSparkIntegrationTest.java:148)
	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:568)
	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:568)
	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@f563fc1)
	- 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@51b274ce)
	- 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@19b656b0)
	- 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$$Lambda$2185/0x0000000801a36a48, org.apache.spark.rdd.RDD$$Lambda$2185/0x0000000801a36a48@3b22cae9)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2186/0x0000000801a36e18, org.apache.spark.rdd.RDD$$Lambda$2186/0x0000000801a36e18@5191288e)
	at org.apache.spark.serializer.SerializationDebugger$.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

testBQSRSparkCloud[6](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.testBQSRSparkCloud(BaseRecalibratorSparkIntegrationTest.java:148)
	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:568)
	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:568)
	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@3c10ba31)
	- 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@2a8ff32)
	- 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@4c0e2715)
	- 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$$Lambda$2185/0x0000000801a36a48, org.apache.spark.rdd.RDD$$Lambda$2185/0x0000000801a36a48@162c02a2)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2186/0x0000000801a36e18, org.apache.spark.rdd.RDD$$Lambda$2186/0x0000000801a36e18@54077082)
	at org.apache.spark.serializer.SerializationDebugger$.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
testBQSRFailWithIncompatibleReference 0.118s passed
testBQSRFailWithoutDBSNP 0.070s passed
testBQSRSparkCloud[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 2.737s failed
testBQSRSparkCloud[1](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq')) 1.224s failed
testBQSRSparkCloud[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 1.230s failed
testBQSRSparkCloud[3](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')) 1.208s failed
testBQSRSparkCloud[4](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')) 1.185s failed
testBQSRSparkCloud[5](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')) 1.134s failed
testBQSRSparkCloud[6](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')) 1.226s failed

Standard output

--------------------------------------------------------------------------------
[20:49:01] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRFailWithIncompatibleReference
--------------------------------------------------------------------------------
[20:49:01] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRFailWithoutDBSNP
--------------------------------------------------------------------------------
[20:49:01] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq
--------------------------------------------------------------------------------
[20:49:04] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq
--------------------------------------------------------------------------------
[20:49:05] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud-
--------------------------------------------------------------------------------
[20:49:06] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --indels-context-size 4
--------------------------------------------------------------------------------
[20:49:07] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --low-quality-tail 5
--------------------------------------------------------------------------------
[20:49:09] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --quantizing-levels 6
--------------------------------------------------------------------------------
[20:49:10] Executing test BaseRecalibratorSparkIntegrationTest:testBQSRSparkCloud--indels --enable-baq --mismatches-context-size 4

Standard error

[June 12, 2025 at 8:49:01 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=874512384
[June 12, 2025 at 8:49:04 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=874512384
[June 12, 2025 at 8:49:05 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=874512384
[June 12, 2025 at 8:49:06 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=874512384
[June 12, 2025 at 8:49:07 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=874512384
[June 12, 2025 at 8:49:09 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=874512384
[June 12, 2025 at 8:49:10 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=874512384
[June 12, 2025 at 8:49:11 PM UTC] org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=874512384