Class org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest

all > org.broadinstitute.hellbender.engine > MultiVariantWalkerIntegrationTest

tests

failures

ignored

10.461s

duration

94%

successful

Failed tests
Tests
Standard error

Failed tests

testDuplicateSources

org.testng.TestException: 
Expected exception of type class org.broadinstitute.hellbender.exceptions.UserException but got java.lang.IllegalStateException: Duplicate key /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf (attempted merging values [VCFHeader:
	INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
	INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
	INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
	INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
	contig=<ID=1,length=16000>
	contig=<ID=2,length=16000>
	contig=<ID=3,length=16000>
	contig=<ID=4,length=16000>
	source=SelectVariants
] and [VCFHeader:
	INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
	INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
	INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
	INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
	contig=<ID=1,length=16000>
	contig=<ID=2,length=16000>
	contig=<ID=3,length=16000>
	contig=<ID=4,length=16000>
	source=SelectVariants
])
	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.IllegalStateException: Duplicate key /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf (attempted merging values [VCFHeader:
	INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
	INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
	INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
	INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
	contig=<ID=1,length=16000>
	contig=<ID=2,length=16000>
	contig=<ID=3,length=16000>
	contig=<ID=4,length=16000>
	source=SelectVariants
] and [VCFHeader:
	INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
	INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
	INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
	INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
	contig=<ID=1,length=16000>
	contig=<ID=2,length=16000>
	contig=<ID=3,length=16000>
	contig=<ID=4,length=16000>
	source=SelectVariants
])
	at java.base/java.util.stream.Collectors.duplicateKeyException(Collectors.java:135)
	at java.base/java.util.stream.Collectors.lambda$uniqKeysMapAccumulator$1(Collectors.java:182)
	at java.base/java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
	at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
	at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
	at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
	at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
	at org.broadinstitute.hellbender.engine.MultiVariantDataSource.getSortedSamples(MultiVariantDataSource.java:240)
	at org.broadinstitute.hellbender.engine.MultiVariantDataSource.<init>(MultiVariantDataSource.java:105)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.initializeDrivingVariants(MultiVariantWalker.java:139)
	at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:76)
	at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:736)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.onStartup(MultiVariantWalker.java:54)
	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.engine.MultiVariantWalkerIntegrationTest.testDuplicateSources(MultiVariantWalkerIntegrationTest.java:82)
	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
testDuplicateSources	0.012s	failed
testGetCompatibleHeader	0.016s	passed
testGetConflictingHeader	0.013s	passed
testIteratorOverlapping	0.015s	passed
testNoDictionaryForAllInputs	0.012s	passed
testNoDictionaryForOneInput	0.015s	passed
testNoDictionaryForOnlyInput	0.009s	passed
testVariantOrder[0]([/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf], null, 26)	0.010s	passed
testVariantOrder[1]([/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf], null, 13)	0.010s	passed
testVariantOrder[2]([/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf], null, 26)	0.012s	passed
testVariantOrder[3]([/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_1.vcf, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_2.vcf], null, 26)	0.015s	passed
testVariantOrder[4]([/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf], 1, 14)	0.010s	passed
testVariantOrder[5]([/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf], 1, 7)	0.008s	passed
testVariantOrder[6]([/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf], 1, 14)	0.009s	passed
testVariantOrder[7]([/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf], 2:200-600, 3)	0.009s	passed
testVariantsFromBundleOrder[0](gs://hellbender-test-logs/staging/remoteBundles/remote_bundle_test7dead624-8610-4455-b52e-d4b1aaf39d0adir/remote_bundle.json, 1, 14)	5.270s	passed
testVariantsFromBundleOrder[1](gs://hellbender-test-logs/staging/remoteBundles/remote_bundle_test4e75ae1e-bbea-4153-831e-4fbd5b4b4123dir/remote_bundle.json, 2:200-600, 3)	5.016s	passed

Standard error

15:31:52.605 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.606 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.606 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.606 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.606 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.606 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.606 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.606 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.606 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.606 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.606 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.607 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.607 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.607 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.607 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.607 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.607 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.608 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:31:52.609 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:31:52.613 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.621 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.621 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.621 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.621 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.621 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.621 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.621 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.621 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.621 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.622 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.622 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.622 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.622 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.622 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.622 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.622 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.622 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.623 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:31:52.625 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf
15:31:52.627 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.627 INFO  ProgressMeter - Starting traversal
15:31:52.627 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.630 INFO  ProgressMeter -             unmapped              0.0                    26         520000.0
15:31:52.630 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:31:52.630 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.637 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.637 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.637 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.637 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.637 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.637 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.637 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.638 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.638 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.638 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.638 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.638 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.638 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.638 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.638 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.638 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.638 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.639 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:31:52.641 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariantsConflictingDictionary.vcf
15:31:52.643 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.649 INFO  TestMultiVariantWalkerIterator - ------------------------------------------------------------
15:31:52.649 INFO  TestMultiVariantWalkerIterator - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.649 INFO  TestMultiVariantWalkerIterator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.649 INFO  TestMultiVariantWalkerIterator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.649 INFO  TestMultiVariantWalkerIterator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.649 INFO  TestMultiVariantWalkerIterator - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.649 INFO  TestMultiVariantWalkerIterator - ------------------------------------------------------------
15:31:52.650 INFO  TestMultiVariantWalkerIterator - ------------------------------------------------------------
15:31:52.650 INFO  TestMultiVariantWalkerIterator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.650 INFO  TestMultiVariantWalkerIterator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.650 INFO  TestMultiVariantWalkerIterator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.650 INFO  TestMultiVariantWalkerIterator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.650 INFO  TestMultiVariantWalkerIterator - Deflater: IntelDeflater
15:31:52.650 INFO  TestMultiVariantWalkerIterator - Inflater: IntelInflater
15:31:52.650 INFO  TestMultiVariantWalkerIterator - GCS max retries/reopens: 20
15:31:52.650 INFO  TestMultiVariantWalkerIterator - Requester pays: disabled
15:31:52.650 INFO  TestMultiVariantWalkerIterator - Initializing engine
15:31:52.652 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_WithOverlap.vcf
15:31:52.654 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_WithOverlap.vcf
15:31:52.656 INFO  TestMultiVariantWalkerIterator - Done initializing engine
15:31:52.656 INFO  ProgressMeter - Starting traversal
15:31:52.656 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.659 INFO  ProgressMeter -             unmapped              0.0                    28         560000.0
15:31:52.659 INFO  ProgressMeter - Traversal complete. Processed 28 total variants in 0.0 minutes.
15:31:52.659 INFO  TestMultiVariantWalkerIterator - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalkerIterator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.666 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.666 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.666 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.666 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.666 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.666 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.666 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.666 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.666 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.667 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.667 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.667 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.667 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.667 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.667 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.667 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.667 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.668 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_NoDict.vcf
15:31:52.670 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_NoDict.vcf
15:31:52.671 WARN  MultiVariantDataSource - A sequence dictionary is required for each input when using multiple inputs, and one could not be obtained for feature input: /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_NoDict.vcf. The input may not exist or may not have a valid header
15:31:52.671 WARN  MultiVariantDataSource - A sequence dictionary is required for each input when using multiple inputs, and one could not be obtained for feature input: /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_NoDict.vcf. The input may not exist or may not have a valid header
15:31:52.671 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.680 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.680 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.680 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.680 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.680 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.680 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.680 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.680 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.680 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.681 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.681 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.681 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.681 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.681 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.681 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.681 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.681 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.682 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:31:52.683 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_NoDict.vcf
15:31:52.684 WARN  MultiVariantDataSource - A sequence dictionary is required for each input when using multiple inputs, and one could not be obtained for feature input: /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_NoDict.vcf. The input may not exist or may not have a valid header
15:31:52.685 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.685 INFO  ProgressMeter - Starting traversal
15:31:52.685 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.686 INFO  ProgressMeter -             unmapped              0.0                    26        1560000.0
15:31:52.686 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:31:52.686 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.692 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.692 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.692 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.692 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.692 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.692 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.692 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.692 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.693 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.693 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.693 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.693 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.693 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.693 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.693 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.693 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.693 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.694 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_NoDict.vcf
15:31:52.695 WARN  MultiVariantDataSource - A sequence dictionary is required for each input when using multiple inputs, and one could not be obtained for feature input: /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_NoDict.vcf. The input may not exist or may not have a valid header
15:31:52.695 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.695 INFO  ProgressMeter - Starting traversal
15:31:52.695 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.695 INFO  ProgressMeter -             unmapped              0.0                    13         Infinity
15:31:52.695 INFO  ProgressMeter - Traversal complete. Processed 13 total variants in 0.0 minutes.
15:31:52.695 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.702 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.702 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.702 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.702 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.702 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.702 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.702 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.702 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.702 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.702 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.702 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.702 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.703 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.703 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.703 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.703 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.703 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.703 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:31:52.704 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.704 INFO  ProgressMeter - Starting traversal
15:31:52.705 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.705 INFO  ProgressMeter -             unmapped              0.0                    26         Infinity
15:31:52.706 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:31:52.706 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.712 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.712 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.712 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.712 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.712 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.712 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.712 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.712 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.712 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.712 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.712 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.712 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.713 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.713 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.713 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.713 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.713 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.714 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:31:52.715 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.715 INFO  ProgressMeter - Starting traversal
15:31:52.715 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.716 INFO  ProgressMeter -             unmapped              0.0                    13         780000.0
15:31:52.716 INFO  ProgressMeter - Traversal complete. Processed 13 total variants in 0.0 minutes.
15:31:52.716 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.722 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.722 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.722 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.722 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.722 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.722 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.722 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.722 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.722 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.722 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.722 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.722 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.722 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.722 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.723 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.723 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.723 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.723 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:31:52.725 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf
15:31:52.726 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.726 INFO  ProgressMeter - Starting traversal
15:31:52.726 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.727 INFO  ProgressMeter -             unmapped              0.0                    26        1560000.0
15:31:52.728 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:31:52.728 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.734 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.734 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.734 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.734 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.734 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.734 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.734 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.734 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.735 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.735 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.735 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.735 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.735 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.735 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.735 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.735 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.735 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.737 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_1.vcf
15:31:52.739 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_2.vcf
15:31:52.741 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.741 INFO  ProgressMeter - Starting traversal
15:31:52.741 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.742 INFO  ProgressMeter -             unmapped              0.0                    26        1560000.0
15:31:52.742 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:31:52.742 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.748 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.748 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.749 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.749 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.749 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.749 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.749 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.749 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.749 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.749 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.749 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.749 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.749 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.750 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.750 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.750 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.750 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.750 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:31:52.751 INFO  IntervalArgumentCollection - Processing 16000 bp from intervals
15:31:52.752 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.752 INFO  ProgressMeter - Starting traversal
15:31:52.752 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.752 INFO  ProgressMeter -             unmapped              0.0                    14         Infinity
15:31:52.753 INFO  ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
15:31:52.753 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.757 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.757 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.757 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.757 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.757 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.757 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.757 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.758 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.758 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.758 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.758 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.758 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.758 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.758 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.758 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.758 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.758 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.759 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:31:52.760 INFO  IntervalArgumentCollection - Processing 16000 bp from intervals
15:31:52.760 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.760 INFO  ProgressMeter - Starting traversal
15:31:52.760 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.760 INFO  ProgressMeter -             unmapped              0.0                     7         Infinity
15:31:52.760 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
15:31:52.760 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.764 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.764 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.765 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.765 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.765 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.765 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.765 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.765 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.765 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.765 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.765 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.765 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.765 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.765 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.766 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.766 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.766 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.766 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:31:52.767 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf
15:31:52.769 INFO  IntervalArgumentCollection - Processing 16000 bp from intervals
15:31:52.769 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.769 INFO  ProgressMeter - Starting traversal
15:31:52.769 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.770 INFO  ProgressMeter -             unmapped              0.0                    14         840000.0
15:31:52.770 INFO  ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
15:31:52.770 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:52.774 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.774 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:52.774 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:52.774 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:52.774 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:52.774 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:52 PM UTC
15:31:52.774 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.774 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:52.775 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:52.775 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:52.775 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:52.775 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:52.775 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:52.775 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:52.775 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:52.775 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:52.775 INFO  TestMultiVariantWalker - Initializing engine
15:31:52.776 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:31:52.777 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf
15:31:52.778 INFO  IntervalArgumentCollection - Processing 401 bp from intervals
15:31:52.778 INFO  TestMultiVariantWalker - Done initializing engine
15:31:52.778 INFO  ProgressMeter - Starting traversal
15:31:52.778 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:31:52.779 INFO  ProgressMeter -             unmapped              0.0                     3         180000.0
15:31:52.779 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:31:52.779 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:31:52 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1015021568
15:31:57.467 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:57.468 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:31:57.468 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:31:57.468 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:31:57.468 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:31:57.468 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:31:57 PM UTC
15:31:57.468 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:57.468 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:31:57.469 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:31:57.469 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:31:57.469 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:31:57.469 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:31:57.469 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:31:57.469 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:31:57.469 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:31:57.469 INFO  TestMultiVariantWalker - Requester pays: disabled
15:31:57.469 INFO  TestMultiVariantWalker - Initializing engine
15:31:59.520 INFO  FeatureManager - Using codec VCFCodec to read file gs://hellbender-test-logs/staging/remoteBundles/remote_bundle_test7dead624-8610-4455-b52e-d4b1aaf39d0adir/interleavedVariants_1.vcf
15:32:01.555 INFO  FeatureManager - Using codec VCFCodec to read file gs://hellbender-test-logs/staging/remoteBundles/remote_bundle_test7dead624-8610-4455-b52e-d4b1aaf39d0adir/interleavedVariants_2.vcf
15:32:02.481 INFO  IntervalArgumentCollection - Processing 16000 bp from intervals
15:32:02.481 INFO  TestMultiVariantWalker - Done initializing engine
15:32:02.481 INFO  ProgressMeter - Starting traversal
15:32:02.481 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:32:02.728 INFO  ProgressMeter -             unmapped              0.0                    14           3428.6
15:32:02.728 INFO  ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
15:32:02.728 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:32:02 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1015021568
15:32:02.735 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:32:02.735 INFO  TestMultiVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
15:32:02.735 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:32:02.735 INFO  TestMultiVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:32:02.735 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:32:02.735 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:32:02 PM UTC
15:32:02.735 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:32:02.735 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:32:02.736 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:32:02.736 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:32:02.736 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:32:02.736 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:32:02.736 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:32:02.736 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:32:02.736 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:32:02.736 INFO  TestMultiVariantWalker - Requester pays: disabled
15:32:02.736 INFO  TestMultiVariantWalker - Initializing engine
15:32:03.885 INFO  FeatureManager - Using codec VCFCodec to read file gs://hellbender-test-logs/staging/remoteBundles/remote_bundle_test4e75ae1e-bbea-4153-831e-4fbd5b4b4123dir/interleavedVariants_1.vcf
15:32:05.852 INFO  FeatureManager - Using codec VCFCodec to read file gs://hellbender-test-logs/staging/remoteBundles/remote_bundle_test4e75ae1e-bbea-4153-831e-4fbd5b4b4123dir/interleavedVariants_2.vcf
15:32:07.138 INFO  IntervalArgumentCollection - Processing 401 bp from intervals
15:32:07.139 INFO  TestMultiVariantWalker - Done initializing engine
15:32:07.139 INFO  ProgressMeter - Starting traversal
15:32:07.139 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:32:07.744 INFO  ProgressMeter -             unmapped              0.0                     3            297.5
15:32:07.744 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:32:07.744 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:32:07 PM UTC] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1015021568