Class org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgenTest
Failed tests
testEmptyPgenExceptionVETS
org.testng.TestException:
Expected exception of type class org.broadinstitute.pgen.PgenEmptyPgenException but got java.lang.NullPointerException: Cannot invoke "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.getContigName()" because the return value of "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.valueOfIndex(int)" is null
at app//org.testng.internal.invokers.ExpectedExceptionsHolder.wrongException(ExpectedExceptionsHolder.java:67)
at app//org.testng.internal.invokers.TestInvoker.considerExceptions(TestInvoker.java:863)
at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:731)
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.lang.NullPointerException: Cannot invoke "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.getContigName()" because the return value of "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.valueOfIndex(int)" is null
at org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils.decodeContig(SchemaUtils.java:125)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.addToVetSortingCollection(ExtractCohortEngine.java:429)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.createVariantIterablesFromUnsortedAvroRanges(ExtractCohortEngine.java:1238)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.traverse(ExtractCohortEngine.java:298)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohort.traverse(ExtractCohort.java:531)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgenTest.testEmptyPgenExceptionVETS(ExtractCohortToPgenTest.java:326)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
... 40 more
testFinalVETSPgenfromRangesAvro
java.lang.NullPointerException: Cannot invoke "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.getContigName()" because the return value of "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.valueOfIndex(int)" is null
at org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils.decodeContig(SchemaUtils.java:125)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.addToVetSortingCollection(ExtractCohortEngine.java:429)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.createVariantIterablesFromUnsortedAvroRanges(ExtractCohortEngine.java:1238)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.traverse(ExtractCohortEngine.java:298)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohort.traverse(ExtractCohort.java:531)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgenTest.testFinalVETSPgenfromRangesAvro(ExtractCohortToPgenTest.java:107)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFinalVETSPgenfromRangesAvroEmptyPgenAllow
java.lang.NullPointerException: Cannot invoke "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.getContigName()" because the return value of "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.valueOfIndex(int)" is null
at org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils.decodeContig(SchemaUtils.java:125)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.addToVetSortingCollection(ExtractCohortEngine.java:429)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.createVariantIterablesFromUnsortedAvroRanges(ExtractCohortEngine.java:1238)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.traverse(ExtractCohortEngine.java:298)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohort.traverse(ExtractCohort.java:531)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgenTest.testFinalVETSPgenfromRangesAvroEmptyPgenAllow(ExtractCohortToPgenTest.java:251)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFinalVETSPgenfromRangesAvroLowAlleleCountMax
java.lang.NullPointerException: Cannot invoke "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.getContigName()" because the return value of "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.valueOfIndex(int)" is null
at org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils.decodeContig(SchemaUtils.java:125)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.addToVetSortingCollection(ExtractCohortEngine.java:429)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.createVariantIterablesFromUnsortedAvroRanges(ExtractCohortEngine.java:1238)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.traverse(ExtractCohortEngine.java:298)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohort.traverse(ExtractCohort.java:531)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgenTest.testFinalVETSPgenfromRangesAvroLowAlleleCountMax(ExtractCohortToPgenTest.java:155)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFinalVETSPgenfromRangesAvroSeparateIndex
java.lang.NullPointerException: Cannot invoke "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.getContigName()" because the return value of "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.valueOfIndex(int)" is null
at org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils.decodeContig(SchemaUtils.java:125)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.addToVetSortingCollection(ExtractCohortEngine.java:429)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.createVariantIterablesFromUnsortedAvroRanges(ExtractCohortEngine.java:1238)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.traverse(ExtractCohortEngine.java:298)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohort.traverse(ExtractCohort.java:531)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgenTest.testFinalVETSPgenfromRangesAvroSeparateIndex(ExtractCohortToPgenTest.java:205)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFinalVQSRPgenfromRangesAvro
java.lang.NullPointerException: Cannot invoke "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.getContigName()" because the return value of "org.broadinstitute.hellbender.tools.gvs.common.ChromosomeEnum.valueOfIndex(int)" is null
at org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils.decodeContig(SchemaUtils.java:125)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.addToVetSortingCollection(ExtractCohortEngine.java:429)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.createVariantIterablesFromUnsortedAvroRanges(ExtractCohortEngine.java:1238)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.traverse(ExtractCohortEngine.java:298)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohort.traverse(ExtractCohort.java:531)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgenTest.testFinalVQSRPgenfromRangesAvro(ExtractCohortToPgenTest.java:299)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Tests
| Test |
Duration |
Result |
| testEmptyPgenExceptionVETS |
1.925s |
failed |
| testFakeFilteringErrorVETS |
0.191s |
passed |
| testFakeFilteringErrorVQSR |
0.205s |
passed |
| testFinalVETSPgenfromRangesAvro |
0.645s |
failed |
| testFinalVETSPgenfromRangesAvroEmptyPgenAllow |
0.553s |
failed |
| testFinalVETSPgenfromRangesAvroLowAlleleCountMax |
0.534s |
failed |
| testFinalVETSPgenfromRangesAvroSeparateIndex |
0.509s |
failed |
| testFinalVQSRPgenfromRangesAvro |
0.507s |
failed |
| testNoFilteringThresholdsErrorVETS |
0.165s |
passed |
| testNoFilteringThresholdsErrorVQSR |
0.202s |
passed |
| testThrowErrorIfNoCallingFilteredGtsAndFilteringBySite |
0.155s |
passed |
| testThrowFilterErrorVETS |
0.145s |
passed |
| testThrowFilterErrorVQSR |
0.127s |
passed |
Standard error
[March 4, 2026 at 3:16:29 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:29 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:29 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:30 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:31 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:31 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:32 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:32 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:32 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:33 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:33 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:33 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:33 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToPgen done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064