Class org.broadinstitute.hellbender.tools.walkers.ReadAnonymizerIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers > ReadAnonymizerIntegrationTest
4

tests
0

failures
0

ignored
1.568s

duration
100%

successful

Tests

Test Duration Result
testReadAnonymizer[0](/home/runner/work/gatk/gatk/src/test/resources/read_anonymizer_test.sam, /home/runner/work/gatk/gatk/src/test/resources/read_anonymizer_expected.sam) 1.411s passed
testTmpDirArgument[0](/tmp/local12542579939630629552) 0.122s passed
testTmpDirArgument[1](file:///tmp/local217893545855830237525/) 0.010s passed
testTmpDirArgument[2](jimfs://f58c056c-d6bc-454e-b1a4-02fbb0235c77/work/tmp/) 0.025s passed

Standard error

18:57:43.999 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.8.11/13f95ee601084b8bf047b2a37f6ea36cd588b96b/gkl-0.8.11.jar!/com/intel/gkl/native/libgkl_compression.so
18:57:44.021 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.024 INFO  TestCreateTempPathClp - org.broadinstitute.hellbender.cmdline vUnavailable
18:57:44.024 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
18:57:44.024 INFO  TestCreateTempPathClp - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:57:44.024 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:57:44.025 INFO  TestCreateTempPathClp - Start Date/Time: May 19, 2025 at 6:57:43 PM UTC
18:57:44.025 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.025 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.026 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:57:44.026 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:57:44.026 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:57:44.027 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:57:44.027 INFO  TestCreateTempPathClp - Deflater: IntelDeflater
18:57:44.027 INFO  TestCreateTempPathClp - Inflater: IntelInflater
18:57:44.027 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
18:57:44.027 INFO  TestCreateTempPathClp - Requester pays: disabled
18:57:44.028 INFO  TestCreateTempPathClp - Initializing engine
18:57:44.028 INFO  TestCreateTempPathClp - Done initializing engine
18:57:44.029 INFO  TestCreateTempPathClp - Shutting down engine
[May 19, 2025 at 6:57:44 PM UTC] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
18:57:44.042 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.042 INFO  TestCreateTempPathClp - org.broadinstitute.hellbender.cmdline vUnavailable
18:57:44.042 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
18:57:44.043 INFO  TestCreateTempPathClp - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:57:44.043 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:57:44.043 INFO  TestCreateTempPathClp - Start Date/Time: May 19, 2025 at 6:57:44 PM UTC
18:57:44.043 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.043 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.044 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:57:44.044 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:57:44.044 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:57:44.044 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:57:44.044 INFO  TestCreateTempPathClp - Deflater: IntelDeflater
18:57:44.044 INFO  TestCreateTempPathClp - Inflater: IntelInflater
18:57:44.044 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
18:57:44.045 INFO  TestCreateTempPathClp - Requester pays: disabled
18:57:44.045 INFO  TestCreateTempPathClp - Initializing engine
18:57:44.045 INFO  TestCreateTempPathClp - Done initializing engine
18:57:44.045 INFO  TestCreateTempPathClp - Shutting down engine
[May 19, 2025 at 6:57:44 PM UTC] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
18:57:44.050 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:?]
18:57:44.065 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.065 INFO  TestCreateTempPathClp - org.broadinstitute.hellbender.cmdline vUnavailable
18:57:44.065 INFO  TestCreateTempPathClp - For support and documentation go to https://software.broadinstitute.org/gatk/
18:57:44.065 INFO  TestCreateTempPathClp - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:57:44.065 INFO  TestCreateTempPathClp - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:57:44.066 INFO  TestCreateTempPathClp - Start Date/Time: May 19, 2025 at 6:57:44 PM UTC
18:57:44.066 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.066 INFO  TestCreateTempPathClp - ------------------------------------------------------------
18:57:44.066 INFO  TestCreateTempPathClp - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:57:44.066 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:57:44.066 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:57:44.067 INFO  TestCreateTempPathClp - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:57:44.067 INFO  TestCreateTempPathClp - Deflater: IntelDeflater
18:57:44.067 INFO  TestCreateTempPathClp - Inflater: IntelInflater
18:57:44.067 INFO  TestCreateTempPathClp - GCS max retries/reopens: 20
18:57:44.067 INFO  TestCreateTempPathClp - Requester pays: disabled
18:57:44.067 INFO  TestCreateTempPathClp - Initializing engine
18:57:44.067 INFO  TestCreateTempPathClp - Done initializing engine
18:57:44.070 INFO  TestCreateTempPathClp - Shutting down engine
[May 19, 2025 at 6:57:44 PM UTC] org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest$TestCreateTempPathClp done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 6:57:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000