Class org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark.pipelines > BQSRPipelineSparkIntegrationTest

tests

failures

ignored

0.904s

duration

successful

Failed tests
Tests
Standard error

Failed tests

testBQSRLocalRef[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --use-original-qualities false'))

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.pipelines.BQSRPipelineSpark.runTool(BQSRPipelineSpark.java:116)
	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.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest.testBQSRLocalRef(BQSRPipelineSparkIntegrationTest.java:96)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569)
	at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base@17.0.12/java.util.ArrayList.forEach(ArrayList.java:1511)
	at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
	at app//org.testng.TestRunner.run(TestRunner.java:602)
	at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at app//org.testng.TestNG.runSuites(TestNG.java:1099)
	at app//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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.12/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 app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@751e396b)
	- 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@529238da)
	- 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@36d30873)
	- 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$$Lambda$2984/0x00007f354cf7b910, org.apache.spark.rdd.RDD$$Lambda$2984/0x00007f354cf7b910@4ed8744c)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2985/0x00007f354cf7f000, org.apache.spark.rdd.RDD$$Lambda$2985/0x00007f354cf7f000@18c02a3)
	at org.apache.spark.serializer.SerializationDebugger$.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)
	... 79 more

testBQSRLocalRef[1](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'))

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.pipelines.BQSRPipelineSpark.runTool(BQSRPipelineSpark.java:116)
	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.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest.testBQSRLocalRef(BQSRPipelineSparkIntegrationTest.java:96)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569)
	at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base@17.0.12/java.util.ArrayList.forEach(ArrayList.java:1511)
	at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
	at app//org.testng.TestRunner.run(TestRunner.java:602)
	at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at app//org.testng.TestNG.runSuites(TestNG.java:1099)
	at app//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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.12/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 app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@7ee4d5f3)
	- 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@139b4348)
	- 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@3aaffd63)
	- 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$$Lambda$2984/0x00007f354cf7b910, org.apache.spark.rdd.RDD$$Lambda$2984/0x00007f354cf7b910@5301876d)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2985/0x00007f354cf7f000, org.apache.spark.rdd.RDD$$Lambda$2985/0x00007f354cf7f000@6962596)
	at org.apache.spark.serializer.SerializationDebugger$.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)
	... 79 more

testBQSRLocalRef[2](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'))

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.pipelines.BQSRPipelineSpark.runTool(BQSRPipelineSpark.java:116)
	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.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest.testBQSRLocalRef(BQSRPipelineSparkIntegrationTest.java:96)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569)
	at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base@17.0.12/java.util.ArrayList.forEach(ArrayList.java:1511)
	at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
	at app//org.testng.TestRunner.run(TestRunner.java:602)
	at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at app//org.testng.TestNG.runSuites(TestNG.java:1099)
	at app//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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.12/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 app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: java.io.NotSerializableException: org.reflections.Reflections
Serialization stack:
	- object not serializable (class: org.reflections.Reflections, value: org.reflections.Reflections@4cb8903f)
	- 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@642e5835)
	- 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@70da133e)
	- 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$$Lambda$2984/0x00007f354cf7b910, org.apache.spark.rdd.RDD$$Lambda$2984/0x00007f354cf7b910@1a7d979d)
	- element of array (index: 0)
	- array (class [Ljava.lang.Object;, size 1)
	- field (class: java.lang.invoke.SerializedLambda, name: capturedArgs, type: class [Ljava.lang.Object;)
	- object (class java.lang.invoke.SerializedLambda, SerializedLambda[capturingClass=class org.apache.spark.rdd.RDD, functionalInterfaceMethod=scala/Function1.apply:(Ljava/lang/Object;)Ljava/lang/Object;, implementation=invokeStatic org/apache/spark/rdd/RDD.$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$$Lambda$2985/0x00007f354cf7f000, org.apache.spark.rdd.RDD$$Lambda$2985/0x00007f354cf7f000@532daee3)
	at org.apache.spark.serializer.SerializationDebugger$.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)
	... 79 more

Tests

Test	Duration	Result
testBQSRLocalRef[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --use-original-qualities false'))	0.345s	failed
testBQSRLocalRef[1](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'))	0.302s	failed
testBQSRLocalRef[2](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'))	0.257s	failed

Standard error

[June 12, 2025 at 8:59:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=916455424
[June 12, 2025 at 8:59:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=916455424
[June 12, 2025 at 8:59:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=916455424