Class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModelIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.vqsr.scalable > TrainVariantAnnotationsModelIntegrationTest

tests

failures

ignored

0.130s

duration

66%

successful

Failed tests
Tests
Standard error

Failed tests

testPositiveAndUnlabeledAnnotationNamesAreNotIdentical

org.testng.TestException: 
Expected exception of type class java.lang.IllegalArgumentException but got java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5
	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@17.0.6/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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.6/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 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.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5
	at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87)
	at org.broadinstitute.hdf5.HDF5File.<init>(HDF5File.java:77)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData.readAnnotationNames(LabeledVariantAnnotationsData.java:229)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel.validateArgumentsAndSetModes(TrainVariantAnnotationsModel.java:347)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel.doWork(TrainVariantAnnotationsModel.java:323)
	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.walkers.vqsr.scalable.TrainVariantAnnotationsModelIntegrationTest.testPositiveAndUnlabeledAnnotationNamesAreNotIdentical(TrainVariantAnnotationsModelIntegrationTest.java:305)
	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)
	... 40 more

Tests

Test	Duration	Result
assertThatExpectedOutputUpdateToggleIsDisabled	0s	passed
testInGatkLiteDocker	0.061s	passed
testPositiveAndUnlabeledAnnotationNamesAreNotIdentical	0.069s	failed

Standard error

[October 27, 2025 at 5:57:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1000341504
[October 27, 2025 at 5:57:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1000341504