Class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest
Failed tests
testNoResourcesAndExtractUnlabeled
org.broadinstitute.hellbender.exceptions.GATKException: Exception encountered during writing of annotations and metadata (org.broadinstitute.hdf5.HDF5LibException: Cannot load the required HDF5 library. HDF5 is currently supported on x86-64 architecture and Linux or OSX systems.). Output file at /tmp/extract15607383586505136341/test.unlabeled.annot.hdf5 may be in a bad state.
at app//org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData.writeHDF5(LabeledVariantAnnotationsData.java:220)
at app//org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations.writeUnlabeledAnnotationsToHDF5(ExtractVariantAnnotations.java:390)
at app//org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations.afterNthPass(ExtractVariantAnnotations.java:347)
at app//org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44)
at app//org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
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:112)
at app//org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest.testNoResourcesAndExtractUnlabeled(ExtractVariantAnnotationsIntegrationTest.java:208)
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 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@17.0.6/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$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testNoResources |
0.152s |
passed |
| testNoResourcesAndExtractUnlabeled |
0.162s |
failed |
| testNoVariantsInInput |
0.134s |
passed |
| testReservedSNPResourceLabel |
0.094s |
passed |
Standard error
[October 27, 2025 at 5:57:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1000341504
java.lang.UnsatisfiedLinkError: /tmp/libjhdf5.2.11.016875001102859387809.so: /tmp/libjhdf5.2.11.016875001102859387809.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform)
at java.base/jdk.internal.loader.NativeLibraries.load(Native Method)
at java.base/jdk.internal.loader.NativeLibraries$NativeLibraryImpl.open(NativeLibraries.java:388)
at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:232)
at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:174)
at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2389)
at java.base/java.lang.Runtime.load0(Runtime.java:755)
at java.base/java.lang.System.load(System.java:1953)
at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:290)
at ncsa.hdf.hdf5lib.H5.<clinit>(H5.java:254)
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.writeHDF5(LabeledVariantAnnotationsData.java:193)
at org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations.writeUnlabeledAnnotationsToHDF5(ExtractVariantAnnotations.java:390)
at org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations.afterNthPass(ExtractVariantAnnotations.java:347)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44)
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.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest.testNoResourcesAndExtractUnlabeled(ExtractVariantAnnotationsIntegrationTest.java:208)
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)
java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path: /usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib
at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2429)
at java.base/java.lang.Runtime.loadLibrary0(Runtime.java:818)
at java.base/java.lang.System.loadLibrary(System.java:1989)
at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:316)
at ncsa.hdf.hdf5lib.H5.<clinit>(H5.java:254)
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.writeHDF5(LabeledVariantAnnotationsData.java:193)
at org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations.writeUnlabeledAnnotationsToHDF5(ExtractVariantAnnotations.java:390)
at org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations.afterNthPass(ExtractVariantAnnotations.java:347)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44)
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.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest.testNoResourcesAndExtractUnlabeled(ExtractVariantAnnotationsIntegrationTest.java:208)
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)
[October 27, 2025 at 5:57:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1000341504
[October 27, 2025 at 5:57:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1000341504
[October 27, 2025 at 5:57:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1000341504