Class org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest
Failed tests
testBundleRemoteWithQueryParams
java.nio.file.NoSuchFileException: src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_Bundle.vcf
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
at java.base/java.nio.file.Files.newByteChannel(Files.java:432)
at java.base/java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:422)
at java.base/java.nio.file.Files.newInputStream(Files.java:160)
at org.broadinstitute.hellbender.utils.io.IOUtils.makeReaderMaybeGzipped(IOUtils.java:384)
at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.assertEqualTextFiles(IntegrationTestSpec.java:278)
at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.assertEqualTextFiles(IntegrationTestSpec.java:270)
at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.assertMatchingFiles(IntegrationTestSpec.java:256)
at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:183)
at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:161)
at org.broadinstitute.hellbender.testutils.IntegrationTestSpec.executeTest(IntegrationTestSpec.java:138)
at org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest.testBundleRemoteWithQueryParams(SelectVariantsIntegrationTest.java:1333)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Tests
| Test |
Duration |
Result |
| testBundleRemoteQueryWithVCFAndIndexInSeparateBuckets[0](gs://hellbender/test/resources/large/dbsnp_138.b37.1.1-65M.vcf, gs://hellbender/test/resources/large/dbsnp_138.b37.1.1-65M.vcf.idx, 1:20547, expected/testSelectVariants_BundleWith_idx.vcf) |
22.778s |
passed |
| testBundleRemoteQueryWithVCFAndIndexInSeparateBuckets[1](gs://hellbender/test/resources/large/dbsnp_138.b37.20.21.vcf.blockgz.gz, gs://hellbender/test/resources/large/dbsnp_138.b37.20.21.vcf.blockgz.gz.tbi, 21:10000128, expected/testSelectVariants_BundleWith_tbi.vcf) |
4.363s |
passed |
| testBundleRemoteWithQueryParams |
3.965s |
failed |
| testSampleSelectionOnNio |
1.233s |
passed |
Standard output
--------------------------------------------------------------------------------
[15:47:04] Executing test SelectVariantsIntegrationTest:testBundle
--------------------------------------------------------------------------------
[15:47:19] Executing test SelectVariantsIntegrationTest:testBundle
--------------------------------------------------------------------------------
[15:47:23] Executing test SelectVariantsIntegrationTest:testBundle
Standard error
[May 19, 2025 at 3:47:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.22 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:47:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:47:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=536870912
15:47:27.501 INFO SelectVariants - ------------------------------------------------------------
15:47:27.501 INFO SelectVariants - org.broadinstitute.hellbender.tools.walkers.variantutils vUnavailable
15:47:27.501 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:27.501 INFO SelectVariants - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:47:27.501 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:47:27.502 INFO SelectVariants - Start Date/Time: May 19, 2025 at 3:47:27 PM UTC
15:47:27.502 INFO SelectVariants - ------------------------------------------------------------
15:47:27.502 INFO SelectVariants - ------------------------------------------------------------
15:47:27.502 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:27.502 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:27.502 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:27.502 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:27.502 INFO SelectVariants - Deflater: IntelDeflater
15:47:27.502 INFO SelectVariants - Inflater: IntelInflater
15:47:27.503 INFO SelectVariants - GCS max retries/reopens: 20
15:47:27.503 INFO SelectVariants - Requester pays: disabled
15:47:27.503 INFO SelectVariants - Initializing engine
15:47:27.519 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf
15:47:27.522 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
15:47:27.523 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
15:47:27.523 INFO SelectVariants - Done initializing engine
15:47:27.523 WARN SelectVariants - ***************************************************************************************************************************
15:47:27.523 WARN SelectVariants - * Detected unsorted genotype fields on input. *
15:47:27.523 WARN SelectVariants - * SelectVariants will sort the genotypes on output which could result in slow traversal as it involves genotype parsing. *
15:47:27.524 WARN SelectVariants - ***************************************************************************************************************************
15:47:27.525 INFO SelectVariants - Including sample 'NA11918'
15:47:27.525 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/vcfexample2.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
15:47:27.645 INFO ProgressMeter - Starting traversal
15:47:27.645 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:47:27.659 INFO ProgressMeter - unmapped 0.0 14 64615.4
15:47:27.660 INFO ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
15:47:28.416 INFO SelectVariants - Shutting down engine
[May 19, 2025 at 3:47:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=536870912