Class org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest

all > org.broadinstitute.hellbender.cmdline > CommandLineProgramIntegrationTest
3

tests
0

failures
0

ignored
0.055s

duration
100%

successful

Tests

Test Duration Result
testTmpDirArgument[0](/tmp/local112686274039359815353) 0.014s passed
testTmpDirArgument[1](file:///tmp/local26624662431647559009/) 0.017s passed
testTmpDirArgument[2](jimfs://c03338a3-88a9-47b7-bc99-519339dbf304/work/tmp/) 0.024s passed

Standard error

17:37:06.375 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:37:06.378 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1106866091388762135.so: /tmp/libgkl_compression1106866091388762135.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:06.378 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:37:06.381 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17095782180356804519.so: /tmp/libgkl_compression17095782180356804519.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:06.383 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.383 INFO  TestCreateTempPathClp - org.broadinstitute.hellbender.cmdline vUnavailable
17:37:06.383 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:06.383 INFO  TestCreateTempPathClp - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:06.384 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:06.384 INFO  TestCreateTempPathClp - Start Date/Time: October 27, 2025 at 5:37:06 PM UTC
17:37:06.384 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.384 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.384 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:06.384 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:06.384 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:06.384 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:06.385 INFO  TestCreateTempPathClp - Deflater: JdkDeflater
17:37:06.385 INFO  TestCreateTempPathClp - Inflater: JdkInflater
17:37:06.385 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
17:37:06.385 INFO  TestCreateTempPathClp - Requester pays: disabled
17:37:06.385 INFO  TestCreateTempPathClp - Initializing engine
17:37:06.385 INFO  TestCreateTempPathClp - Done initializing engine
17:37:06.385 INFO  TestCreateTempPathClp - Shutting down engine
[October 27, 2025 at 5:37:06 PM UTC] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:06.388 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:37:06.396 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15162504838027317387.so: /tmp/libgkl_compression15162504838027317387.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:06.396 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:37:06.399 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2567510620383329428.so: /tmp/libgkl_compression2567510620383329428.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:06.401 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.401 INFO  TestCreateTempPathClp - org.broadinstitute.hellbender.cmdline vUnavailable
17:37:06.401 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:06.401 INFO  TestCreateTempPathClp - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:06.401 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:06.402 INFO  TestCreateTempPathClp - Start Date/Time: October 27, 2025 at 5:37:06 PM UTC
17:37:06.402 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.402 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.402 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:06.402 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:06.402 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:06.402 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:06.402 INFO  TestCreateTempPathClp - Deflater: JdkDeflater
17:37:06.402 INFO  TestCreateTempPathClp - Inflater: JdkInflater
17:37:06.402 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
17:37:06.403 INFO  TestCreateTempPathClp - Requester pays: disabled
17:37:06.403 INFO  TestCreateTempPathClp - Initializing engine
17:37:06.403 INFO  TestCreateTempPathClp - Done initializing engine
17:37:06.403 INFO  TestCreateTempPathClp - Shutting down engine
[October 27, 2025 at 5:37:06 PM UTC] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:06.406 WARN  TestCreateTempPathClp - Failed to delete temp file for testing temp dir
java.lang.NullPointerException: Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null
	at java.base/java.nio.file.Files.provider(Files.java:105) ~[?:?]
	at java.base/java.nio.file.Files.deleteIfExists(Files.java:1191) ~[?:?]
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.tryToWriteAnExecutableFileAndWarnOnFailure(CommandLineProgram.java:540) ~[main/:?]
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:173) ~[main/:?]
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) ~[main/:?]
	at org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest.testTmpDirArgument(CommandLineProgramIntegrationTest.java:74) ~[test/:?]
	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) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) ~[testng-7.7.0.jar:7.7.0]
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) [?:?]
	at org.testng.TestRunner.privateRun(TestRunner.java:829) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestRunner.run(TestRunner.java:602) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunner.run(SuiteRunner.java:330) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestNG.runSuites(TestNG.java:1099) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestNG.run(TestNG.java:1067) [testng-7.7.0.jar:7.7.0]
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) [gradle-testing-jvm-infrastructure-8.10.2.jar:8.10.2]
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) [gradle-testing-jvm-infrastructure-8.10.2.jar:8.10.2]
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
	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) [gradle-messaging-8.10.2.jar:8.10.2]
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) [gradle-messaging-8.10.2.jar:8.10.2]
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) [gradle-messaging-8.10.2.jar:8.10.2]
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) [gradle-messaging-8.10.2.jar:8.10.2]
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) [?:?]
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) [gradle-testing-base-infrastructure-8.10.2.jar:8.10.2]
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) [gradle-worker-main-8.10.2.jar:8.10.2]
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) [gradle-worker-main-8.10.2.jar:8.10.2]
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) [gradle-worker-main-8.10.2.jar:8.10.2]
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) [gradle-worker.jar:?]
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74) [gradle-worker.jar:?]
17:37:06.415 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:37:06.418 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4394012019377710541.so: /tmp/libgkl_compression4394012019377710541.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:06.418 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:37:06.421 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression14836219417968488592.so: /tmp/libgkl_compression14836219417968488592.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:06.423 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.423 INFO  TestCreateTempPathClp - org.broadinstitute.hellbender.cmdline vUnavailable
17:37:06.423 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:06.423 INFO  TestCreateTempPathClp - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:06.423 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:06.423 INFO  TestCreateTempPathClp - Start Date/Time: October 27, 2025 at 5:37:06 PM UTC
17:37:06.423 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.423 INFO  TestCreateTempPathClp - ------------------------------------------------------------
17:37:06.424 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:06.424 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:06.424 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:06.424 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:06.424 INFO  TestCreateTempPathClp - Deflater: JdkDeflater
17:37:06.424 INFO  TestCreateTempPathClp - Inflater: JdkInflater
17:37:06.425 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
17:37:06.425 INFO  TestCreateTempPathClp - Requester pays: disabled
17:37:06.425 INFO  TestCreateTempPathClp - Initializing engine
17:37:06.425 INFO  TestCreateTempPathClp - Done initializing engine
17:37:06.427 INFO  TestCreateTempPathClp - Shutting down engine
[October 27, 2025 at 5:37:06 PM UTC] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000