Class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest
|
3%
successful |
Failed tests
testDifferentThreadValuesFromABucket[0](1)
java.lang.ExceptionInInitializerError at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:756) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:750) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:745) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testDifferentThreadValuesFromABucket(GenomicsDBImportIntegrationTest.java:668) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74) Caused by: org.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library at app//org.genomicsdb.GenomicsDBUtilsJni.<clinit>(GenomicsDBUtilsJni.java:34) ... 63 more Caused by: java.lang.UnsatisfiedLinkError: /tmp/libtiledbgenomicsdb15158697024575330756.so: /tmp/libtiledbgenomicsdb15158697024575330756.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform) at java.base/jdk.internal.loader.NativeLibraries.load(Native Method) at java.base/jdk.internal.loader.NativeLibraries$NativeLibraryImpl.open(NativeLibraries.java:388) at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:232) at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:174) at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2389) at java.base/java.lang.Runtime.load0(Runtime.java:755) at java.base/java.lang.System.load(System.java:1953) at org.genomicsdb.GenomicsDBLibLoader.loadLibraryFromJar(GenomicsDBLibLoader.java:155) at org.genomicsdb.GenomicsDBLibLoader.loadLibrary(GenomicsDBLibLoader.java:54) at org.genomicsdb.GenomicsDBUtilsJni.<clinit>(GenomicsDBUtilsJni.java:31) ... 63 more
testDifferentThreadValuesFromABucket[1](2)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:756) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:750) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:745) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testDifferentThreadValuesFromABucket(GenomicsDBImportIntegrationTest.java:668) 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)
testDifferentThreadValuesFromABucket[2](5)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:756) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:750) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:745) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testDifferentThreadValuesFromABucket(GenomicsDBImportIntegrationTest.java:668) 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)
testExplicitIndicesInSampleNameMapInTheCloud[0](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.gz.tbi HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.gz.tbi )
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testExplicitIndicesInSampleNameMapInTheCloud(GenomicsDBImportIntegrationTest.java:1166) 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)
testExplicitIndicesInSampleNameMapInTheCloud[1](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.idx HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.idx )
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testExplicitIndicesInSampleNameMapInTheCloud(GenomicsDBImportIntegrationTest.java:1166) 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)
testExplicitIndicesInSampleNameMapInTheCloud[2](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf.gz HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf.gz )
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testExplicitIndicesInSampleNameMapInTheCloud(GenomicsDBImportIntegrationTest.java:1166) 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)
testExplicitIndicesInSampleNameMapInTheCloud[3](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf )
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testExplicitIndicesInSampleNameMapInTheCloud(GenomicsDBImportIntegrationTest.java:1166) 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)
testExplicitIndicesInSampleNameMapInTheCloud[4](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.gz.tbi HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.gz.tbi )
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testExplicitIndicesInSampleNameMapInTheCloud(GenomicsDBImportIntegrationTest.java:1166) 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)
testExplicitIndicesInSampleNameMapInTheCloud[5](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.idx HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.idx )
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testExplicitIndicesInSampleNameMapInTheCloud(GenomicsDBImportIntegrationTest.java:1166) 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)
testExplicitIndicesInSampleNameMapInTheCloud[6](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf.gz HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf.gz )
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testExplicitIndicesInSampleNameMapInTheCloud(GenomicsDBImportIntegrationTest.java:1166) 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)
testExplicitIndicesInSampleNameMapInTheCloud[7](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf )
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testExplicitIndicesInSampleNameMapInTheCloud(GenomicsDBImportIntegrationTest.java:1166) 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)
testGenomicsDBImportGCSInputs
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporter(GenomicsDBImportIntegrationTest.java:702) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporter(GenomicsDBImportIntegrationTest.java:695) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputs(GenomicsDBImportIntegrationTest.java:555) 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)
testGenomicsDBImportGCSInputsInBatchesNativeReader[0](1)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatchesNativeReader(GenomicsDBImportIntegrationTest.java:653) 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)
testGenomicsDBImportGCSInputsInBatchesNativeReader[1](2)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatchesNativeReader(GenomicsDBImportIntegrationTest.java:653) 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)
testGenomicsDBImportGCSInputsInBatchesNativeReader[2](3)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatchesNativeReader(GenomicsDBImportIntegrationTest.java:653) 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)
testGenomicsDBImportGCSInputsInBatchesNativeReader[3](4)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatchesNativeReader(GenomicsDBImportIntegrationTest.java:653) 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)
testGenomicsDBImportGCSInputsInBatchesNativeReader[4](100)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatchesNativeReader(GenomicsDBImportIntegrationTest.java:653) 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)
testGenomicsDBImportGCSInputsInBatches[0](1)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:720) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatches(GenomicsDBImportIntegrationTest.java:648) 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)
testGenomicsDBImportGCSInputsInBatches[1](2)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:720) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatches(GenomicsDBImportIntegrationTest.java:648) 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)
testGenomicsDBImportGCSInputsInBatches[2](3)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:720) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatches(GenomicsDBImportIntegrationTest.java:648) 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)
testGenomicsDBImportGCSInputsInBatches[3](4)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:720) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatches(GenomicsDBImportIntegrationTest.java:648) 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)
testGenomicsDBImportGCSInputsInBatches[4](100)
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:728) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImporterWithBatchSize(GenomicsDBImportIntegrationTest.java:720) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testGenomicsDBImportGCSInputsInBatches(GenomicsDBImportIntegrationTest.java:648) 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)
testWriteToAndQueryFromGCS
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:1045) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:680) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1117) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:784) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:756) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:750) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.writeToGenomicsDB(GenomicsDBImportIntegrationTest.java:745) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testWriteToAndQueryFromGCS(GenomicsDBImportIntegrationTest.java:1651) 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)
testWriteToAndQueryFromGCSUsingConnector
java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.useGcsHdfsConnector(GenomicsDBUtils.java:151) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.initializeWorkspaceAndToolMode(GenomicsDBImport.java:495) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onStartup(GenomicsDBImport.java:475) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:148) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193) at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27) at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.basicWriteAndQueryWithOptions(GenomicsDBImportIntegrationTest.java:1590) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testWriteToAndQueryFromGCSUsingConnector(GenomicsDBImportIntegrationTest.java:1671) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testWriteToExistingGCSDirectory
org.testng.TestException: Expected exception of type class org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport$UnableToCreateGenomicsDBWorkspace but got java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at app//org.testng.internal.invokers.ExpectedExceptionsHolder.wrongException(ExpectedExceptionsHolder.java:67) at app//org.testng.internal.invokers.TestInvoker.considerExceptions(TestInvoker.java:863) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:731) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74) Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.genomicsdb.GenomicsDBUtilsJni at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:47) at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImportIntegrationTest.testWriteToExistingGCSDirectory(GenomicsDBImportIntegrationTest.java:1660) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) ... 40 more
Tests
| Test | Duration | Result |
|---|---|---|
| testDifferentThreadValuesFromABucket[0](1) | 1.953s | failed |
| testDifferentThreadValuesFromABucket[1](2) | 1.259s | failed |
| testDifferentThreadValuesFromABucket[2](5) | 1.138s | failed |
| testExplicitIndicesInSampleNameMapInTheCloud[0](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.gz.tbi HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.gz.tbi ) | 0.412s | failed |
| testExplicitIndicesInSampleNameMapInTheCloud[1](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.idx HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.idx ) | 0.379s | failed |
| testExplicitIndicesInSampleNameMapInTheCloud[2](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf.gz HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf.gz ) | 0.643s | failed |
| testExplicitIndicesInSampleNameMapInTheCloud[3](HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf ) | 0.441s | failed |
| testExplicitIndicesInSampleNameMapInTheCloud[4](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.gz.tbi HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.gz.tbi ) | 0.319s | failed |
| testExplicitIndicesInSampleNameMapInTheCloud[5](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/NA19625.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/NA19625.g.vcf.idx HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00096.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00096.g.vcf.idx ) | 0.382s | failed |
| testExplicitIndicesInSampleNameMapInTheCloud[6](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf.gz HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf.gz gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.gz.tbi HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf.gz ) | 0.432s | failed |
| testExplicitIndicesInSampleNameMapInTheCloud[7](NA19625 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/NA19625.g.vcf HG00268 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_without_indices/HG00268.g.vcf gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcf_indices_only/HG00268.g.vcf.idx HG00096 gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/genomicsdb/gvcfs_with_indices/HG00096.g.vcf ) | 0.363s | failed |
| testGenomicsDBImportGCSInputs | 1.197s | failed |
| testGenomicsDBImportGCSInputsInBatchesNativeReader[0](1) | 1.632s | failed |
| testGenomicsDBImportGCSInputsInBatchesNativeReader[1](2) | 1.733s | failed |
| testGenomicsDBImportGCSInputsInBatchesNativeReader[2](3) | 1.692s | failed |
| testGenomicsDBImportGCSInputsInBatchesNativeReader[3](4) | 1.655s | failed |
| testGenomicsDBImportGCSInputsInBatchesNativeReader[4](100) | 1.647s | failed |
| testGenomicsDBImportGCSInputsInBatches[0](1) | 1.266s | failed |
| testGenomicsDBImportGCSInputsInBatches[1](2) | 1.209s | failed |
| testGenomicsDBImportGCSInputsInBatches[2](3) | 1.140s | failed |
| testGenomicsDBImportGCSInputsInBatches[3](4) | 1.274s | failed |
| testGenomicsDBImportGCSInputsInBatches[4](100) | 1.219s | failed |
| testUnindexedCloudGVCFsAreActuallyUnindexed | 0.149s | passed |
| testWriteToAndQueryFromGCS | 0.077s | failed |
| testWriteToAndQueryFromGCSUsingConnector | 0.064s | failed |
| testWriteToExistingGCSDirectory | 0.001s | failed |
Standard error
[October 27, 2025 at 5:44:39 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:40 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:41 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:42 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:42 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:43 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:43 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:44 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:44 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:44 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:45 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:46 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:47 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:48 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:50 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:51 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:52 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:54 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:55 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:57 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:45:00 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:45:01 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=874512384 [October 27, 2025 at 5:45:01 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=874512384