Class org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest

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

tests
0

failures
0

ignored
0.047s

duration
100%

successful

Tests

Test Duration Result
testTmpDirArgument[0](/tmp/local18711345980483410782) 0.021s passed
testTmpDirArgument[1](file:///tmp/local218034133381648928679/) 0.006s passed
testTmpDirArgument[2](jimfs://5b612ea9-7d23-4ae5-93cd-f28532f66794/work/tmp/) 0.020s passed

Standard error

14:20:40.790 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.798 INFO  TestCreateTempPathClp - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:20:40.799 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
14:20:40.799 INFO  TestCreateTempPathClp - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:20:40.799 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:20:40.799 INFO  TestCreateTempPathClp - Start Date/Time: June 2, 2025 at 2:20:40 PM GMT
14:20:40.799 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.799 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.799 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:20:40.800 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:20:40.800 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:20:40.800 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:20:40.800 INFO  TestCreateTempPathClp - Deflater: IntelDeflater
14:20:40.800 INFO  TestCreateTempPathClp - Inflater: IntelInflater
14:20:40.800 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
14:20:40.800 INFO  TestCreateTempPathClp - Requester pays: disabled
14:20:40.800 INFO  TestCreateTempPathClp - Initializing engine
14:20:40.800 INFO  TestCreateTempPathClp - Done initializing engine
14:20:40.801 INFO  TestCreateTempPathClp - Shutting down engine
[June 2, 2025 at 2:20:40 PM GMT] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
14:20:40.806 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.806 INFO  TestCreateTempPathClp - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:20:40.806 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
14:20:40.806 INFO  TestCreateTempPathClp - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:20:40.806 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:20:40.806 INFO  TestCreateTempPathClp - Start Date/Time: June 2, 2025 at 2:20:40 PM GMT
14:20:40.806 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.806 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.806 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:20:40.807 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:20:40.807 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:20:40.807 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:20:40.807 INFO  TestCreateTempPathClp - Deflater: IntelDeflater
14:20:40.807 INFO  TestCreateTempPathClp - Inflater: IntelInflater
14:20:40.807 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
14:20:40.807 INFO  TestCreateTempPathClp - Requester pays: disabled
14:20:40.807 INFO  TestCreateTempPathClp - Initializing engine
14:20:40.807 INFO  TestCreateTempPathClp - Done initializing engine
14:20:40.808 INFO  TestCreateTempPathClp - Shutting down engine
[June 2, 2025 at 2:20:40 PM GMT] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
14:20:40.811 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) ~[gatk-package-5749ecb-SNAPSHOT-local.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:173) ~[gatk-package-5749ecb-SNAPSHOT-local.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) ~[gatk-package-5749ecb-SNAPSHOT-local.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest.testTmpDirArgument(CommandLineProgramIntegrationTest.java:74) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-test.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	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:569) ~[?:?]
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) ~[gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) [?:?]
	at org.testng.TestRunner.privateRun(TestRunner.java:829) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.TestRunner.run(TestRunner.java:602) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.SuiteRunner.run(SuiteRunner.java:330) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.TestNG.runSuites(TestNG.java:1099) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	at org.testng.TestNG.run(TestNG.java:1067) [gatk-package-4.6.2.0-7-g5749ecb-SNAPSHOT-testDependencies.jar:4.6.2.0-7-g5749ecb-SNAPSHOT]
	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:569) ~[?:?]
	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:?]
14:20:40.822 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.822 INFO  TestCreateTempPathClp - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:20:40.823 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
14:20:40.823 INFO  TestCreateTempPathClp - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:20:40.823 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:20:40.823 INFO  TestCreateTempPathClp - Start Date/Time: June 2, 2025 at 2:20:40 PM GMT
14:20:40.824 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.824 INFO  TestCreateTempPathClp - ------------------------------------------------------------
14:20:40.824 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:20:40.824 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:20:40.824 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:20:40.824 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:20:40.824 INFO  TestCreateTempPathClp - Deflater: IntelDeflater
14:20:40.824 INFO  TestCreateTempPathClp - Inflater: IntelInflater
14:20:40.824 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
14:20:40.825 INFO  TestCreateTempPathClp - Requester pays: disabled
14:20:40.825 INFO  TestCreateTempPathClp - Initializing engine
14:20:40.825 INFO  TestCreateTempPathClp - Done initializing engine
14:20:40.827 INFO  TestCreateTempPathClp - Shutting down engine
[June 2, 2025 at 2:20:40 PM GMT] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000