Class org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest
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0%
successful |
Failed tests
testDenoiseReadCounts[0](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[10](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[11](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[12](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[13](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[14](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[15](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[16](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[17](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[18](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[19](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[1](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[20](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[21](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[22](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 1, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[23](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 10, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[24](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[25](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[26](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[27](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[28](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[29](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[2](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[30](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[31](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[32](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[33](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[34](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[35](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[36](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[37](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[38](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[39](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[3](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[40](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[41](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[42](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[43](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[44](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[45](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[46](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 1, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[47](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 10, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) at jdk.internal.reflect.GeneratedMethodAccessor90.invoke(Unknown Source) 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)
testDenoiseReadCounts[4](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[5](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[6](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[7](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[8](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
testDenoiseReadCounts[9](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true)
java.lang.NoClassDefFoundError: Could not initialize class ncsa.hdf.hdf5lib.H5 at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87) at org.broadinstitute.hdf5.HDF5Library.load(HDF5Library.java:43) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:177) 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:108) at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest.testDenoiseReadCounts(DenoiseReadCountsIntegrationTest.java:71) 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)
Tests
| Test | Duration | Result |
|---|---|---|
| testDenoiseReadCounts[0](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false) | 0.075s | failed |
| testDenoiseReadCounts[10](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true) | 0.075s | failed |
| testDenoiseReadCounts[11](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true) | 0.075s | failed |
| testDenoiseReadCounts[12](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false) | 0.075s | failed |
| testDenoiseReadCounts[13](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true) | 0.076s | failed |
| testDenoiseReadCounts[14](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false) | 0.075s | failed |
| testDenoiseReadCounts[15](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false) | 0.074s | failed |
| testDenoiseReadCounts[16](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false) | 0.074s | failed |
| testDenoiseReadCounts[17](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true) | 0.075s | failed |
| testDenoiseReadCounts[18](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false) | 0.075s | failed |
| testDenoiseReadCounts[19](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false) | 0.075s | failed |
| testDenoiseReadCounts[1](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true) | 0.075s | failed |
| testDenoiseReadCounts[20](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv, true) | 0.075s | failed |
| testDenoiseReadCounts[21](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 0, true) | 0.075s | failed |
| testDenoiseReadCounts[22](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 1, true) | 0.074s | failed |
| testDenoiseReadCounts[23](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 10, true) | 0.074s | failed |
| testDenoiseReadCounts[24](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false) | 0.074s | failed |
| testDenoiseReadCounts[25](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true) | 0.074s | failed |
| testDenoiseReadCounts[26](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false) | 0.073s | failed |
| testDenoiseReadCounts[27](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false) | 0.075s | failed |
| testDenoiseReadCounts[28](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false) | 0.074s | failed |
| testDenoiseReadCounts[29](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true) | 0.072s | failed |
| testDenoiseReadCounts[2](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false) | 0.075s | failed |
| testDenoiseReadCounts[30](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false) | 0.075s | failed |
| testDenoiseReadCounts[31](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false) | 0.075s | failed |
| testDenoiseReadCounts[32](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true) | 0.075s | failed |
| testDenoiseReadCounts[33](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true) | 0.075s | failed |
| testDenoiseReadCounts[34](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true) | 0.074s | failed |
| testDenoiseReadCounts[35](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true) | 0.074s | failed |
| testDenoiseReadCounts[36](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false) | 0.074s | failed |
| testDenoiseReadCounts[37](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true) | 0.075s | failed |
| testDenoiseReadCounts[38](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false) | 0.075s | failed |
| testDenoiseReadCounts[39](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false) | 0.075s | failed |
| testDenoiseReadCounts[3](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false) | 0.074s | failed |
| testDenoiseReadCounts[40](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false) | 0.076s | failed |
| testDenoiseReadCounts[41](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true) | 0.076s | failed |
| testDenoiseReadCounts[42](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false) | 0.075s | failed |
| testDenoiseReadCounts[43](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false) | 0.075s | failed |
| testDenoiseReadCounts[44](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5, true) | 0.075s | failed |
| testDenoiseReadCounts[45](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 0, true) | 0.074s | failed |
| testDenoiseReadCounts[46](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 1, true) | 0.075s | failed |
| testDenoiseReadCounts[47](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 10, true) | 0.076s | failed |
| testDenoiseReadCounts[4](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false) | 0.074s | failed |
| testDenoiseReadCounts[5](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true) | 0.075s | failed |
| testDenoiseReadCounts[6](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false) | 0.075s | failed |
| testDenoiseReadCounts[7](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false) | 0.076s | failed |
| testDenoiseReadCounts[8](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true) | 0.075s | failed |
| testDenoiseReadCounts[9](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true) | 0.075s | failed |
Standard error
[October 27, 2025 at 5:39:32 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:32 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:32 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:33 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:34 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:35 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:36 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:36 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:36 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:36 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [October 27, 2025 at 5:39:36 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600