Class org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcfTest

all > org.broadinstitute.hellbender.tools.gvs.extract > ExtractCohortToVcfTest

tests

failures

ignored

1.269s

duration

77%

successful

Failed tests
Tests
Standard error

Failed tests

testFinalVETSVCFfromRangesAvro

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.ExtractCohortToVcfTest.testFinalVETSVCFfromRangesAvro(ExtractCohortToVcfTest.java:84)
	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)

testFinalVQSRVCFfromRangesAvro

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.ExtractCohortToVcfTest.testFinalVQSRVCFfromRangesAvro(ExtractCohortToVcfTest.java:123)
	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
testFakeFilteringErrorVETS	0.151s	passed
testFakeFilteringErrorVQSR	0.121s	passed
testFinalVETSVCFfromRangesAvro	0.150s	failed
testFinalVQSRVCFfromRangesAvro	0.145s	failed
testNoFilteringThresholdsErrorVETS	0.158s	passed
testNoFilteringThresholdsErrorVQSR	0.152s	passed
testThrowErrorIfNoCallingFilteredGtsAndFilteringBySite	0.144s	passed
testThrowFilterErrorVETS	0.127s	passed
testThrowFilterErrorVQSR	0.121s	passed

Standard error

[March 4, 2026 at 3:16:33 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:33 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:33 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:34 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:34 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:34 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:34 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:34 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064
[March 4, 2026 at 3:16:34 PM GMT] org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortToVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2111832064