Class org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest

all > org.broadinstitute.hellbender.engine > MultiVariantWalkerIntegrationTest

tests

failures

ignored

0.410s

duration

93%

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 /gatkCloneMountPoint/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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569)
	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 /gatkCloneMountPoint/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:569)
	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	0.025s	failed
testGetCompatibleHeader	0.030s	passed
testGetConflictingHeader	0.034s	passed
testIteratorOverlapping	0.039s	passed
testNoDictionaryForAllInputs	0.031s	passed
testNoDictionaryForOneInput	0.025s	passed
testNoDictionaryForOnlyInput	0.027s	passed
testVariantOrder[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf], null, 26)	0.019s	passed
testVariantOrder[1]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf], null, 13)	0.022s	passed
testVariantOrder[2]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf], null, 26)	0.022s	passed
testVariantOrder[3]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_1.vcf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_2.vcf], null, 26)	0.028s	passed
testVariantOrder[4]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf], 1, 14)	0.027s	passed
testVariantOrder[5]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf], 1, 7)	0.026s	passed
testVariantOrder[6]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf], 1, 14)	0.029s	passed
testVariantOrder[7]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf], 2:200-600, 3)	0.026s	passed
testVariantsFromBundleOrder	-	ignored

Standard error

15:47:34.840 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.840 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:34.840 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:34.840 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:34.841 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:34.841 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:34 PM GMT
15:47:34.841 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.841 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.841 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:34.841 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:34.841 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:34.841 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:34.841 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:34.841 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:34.841 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:34.841 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:34.842 INFO  TestMultiVariantWalker - Initializing engine
15:47:34.843 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:47:34.845 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:47:34.849 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:34 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:34.870 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.871 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:34.871 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:34.871 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:34.871 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:34.871 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:34 PM GMT
15:47:34.871 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.871 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.871 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:34.871 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:34.871 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:34.871 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:34.871 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:34.871 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:34.871 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:34.871 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:34.872 INFO  TestMultiVariantWalker - Initializing engine
15:47:34.873 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:47:34.875 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf
15:47:34.877 INFO  TestMultiVariantWalker - Done initializing engine
15:47:34.877 INFO  ProgressMeter - Starting traversal
15:47:34.877 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:34.881 INFO  ProgressMeter -             unmapped              0.0                    26         390000.0
15:47:34.881 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:47:34.881 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:34 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:34.906 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.906 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:34.906 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:34.906 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:34.906 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:34.906 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:34 PM GMT
15:47:34.906 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.906 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.906 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:34.906 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:34.907 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:34.907 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:34.907 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:34.907 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:34.907 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:34.907 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:34.907 INFO  TestMultiVariantWalker - Initializing engine
15:47:34.908 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:47:34.912 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariantsConflictingDictionary.vcf
15:47:34.916 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:34 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:34.938 INFO  TestMultiVariantWalkerIterator - ------------------------------------------------------------
15:47:34.939 INFO  TestMultiVariantWalkerIterator - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:34.939 INFO  TestMultiVariantWalkerIterator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:34.939 INFO  TestMultiVariantWalkerIterator - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:34.939 INFO  TestMultiVariantWalkerIterator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:34.939 INFO  TestMultiVariantWalkerIterator - Start Date/Time: May 19, 2025 at 3:47:34 PM GMT
15:47:34.939 INFO  TestMultiVariantWalkerIterator - ------------------------------------------------------------
15:47:34.939 INFO  TestMultiVariantWalkerIterator - ------------------------------------------------------------
15:47:34.939 INFO  TestMultiVariantWalkerIterator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:34.940 INFO  TestMultiVariantWalkerIterator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:34.940 INFO  TestMultiVariantWalkerIterator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:34.940 INFO  TestMultiVariantWalkerIterator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:34.940 INFO  TestMultiVariantWalkerIterator - Deflater: IntelDeflater
15:47:34.940 INFO  TestMultiVariantWalkerIterator - Inflater: IntelInflater
15:47:34.940 INFO  TestMultiVariantWalkerIterator - GCS max retries/reopens: 20
15:47:34.940 INFO  TestMultiVariantWalkerIterator - Requester pays: disabled
15:47:34.940 INFO  TestMultiVariantWalkerIterator - Initializing engine
15:47:34.942 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_WithOverlap.vcf
15:47:34.944 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_WithOverlap.vcf
15:47:34.948 INFO  TestMultiVariantWalkerIterator - Done initializing engine
15:47:34.948 INFO  ProgressMeter - Starting traversal
15:47:34.948 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:34.956 INFO  ProgressMeter -             unmapped              0.0                    28         210000.0
15:47:34.956 INFO  ProgressMeter - Traversal complete. Processed 28 total variants in 0.0 minutes.
15:47:34.956 INFO  TestMultiVariantWalkerIterator - Shutting down engine
[May 19, 2025 at 3:47:34 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalkerIterator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:34.979 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.979 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:34.979 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:34.979 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:34.979 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:34.979 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:34 PM GMT
15:47:34.979 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.979 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:34.979 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:34.979 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:34.979 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:34.979 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:34.980 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:34.980 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:34.980 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:34.980 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:34.980 INFO  TestMultiVariantWalker - Initializing engine
15:47:34.984 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_NoDict.vcf
15:47:34.986 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_NoDict.vcf
15:47:34.987 WARN  MultiVariantDataSource - A sequence dictionary is required for each input when using multiple inputs, and one could not be obtained for feature input: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_NoDict.vcf. The input may not exist or may not have a valid header
15:47:34.988 WARN  MultiVariantDataSource - A sequence dictionary is required for each input when using multiple inputs, and one could not be obtained for feature input: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_NoDict.vcf. The input may not exist or may not have a valid header
15:47:34.988 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:34 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.006 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.006 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.006 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.006 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.006 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.006 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.006 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.006 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.006 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.006 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.006 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.006 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.006 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.007 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.007 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.007 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.007 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.008 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:47:35.009 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_NoDict.vcf
15:47:35.010 WARN  MultiVariantDataSource - A sequence dictionary is required for each input when using multiple inputs, and one could not be obtained for feature input: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2_NoDict.vcf. The input may not exist or may not have a valid header
15:47:35.011 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.011 INFO  ProgressMeter - Starting traversal
15:47:35.011 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.014 INFO  ProgressMeter -             unmapped              0.0                    26         520000.0
15:47:35.014 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:47:35.014 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.037 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.038 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.038 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.038 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.038 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.038 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.038 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.038 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.038 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.039 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.039 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.039 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.039 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.039 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.039 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.039 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.039 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.040 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_NoDict.vcf
15:47:35.041 WARN  MultiVariantDataSource - A sequence dictionary is required for each input when using multiple inputs, and one could not be obtained for feature input: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1_NoDict.vcf. The input may not exist or may not have a valid header
15:47:35.041 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.041 INFO  ProgressMeter - Starting traversal
15:47:35.041 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.042 INFO  ProgressMeter -             unmapped              0.0                    13         780000.0
15:47:35.042 INFO  ProgressMeter - Traversal complete. Processed 13 total variants in 0.0 minutes.
15:47:35.042 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.058 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.058 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.058 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.058 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.058 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.058 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.058 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.058 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.058 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.058 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.058 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.058 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.059 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.059 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.059 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.059 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.059 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.060 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:47:35.061 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.061 INFO  ProgressMeter - Starting traversal
15:47:35.061 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.062 INFO  ProgressMeter -             unmapped              0.0                    26        1560000.0
15:47:35.062 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:47:35.062 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.081 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.081 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.081 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.081 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.081 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.081 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.081 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.081 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.081 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.081 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.081 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.081 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.081 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.081 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.082 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.082 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.082 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.083 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:47:35.084 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.084 INFO  ProgressMeter - Starting traversal
15:47:35.084 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.085 INFO  ProgressMeter -             unmapped              0.0                    13         780000.0
15:47:35.085 INFO  ProgressMeter - Traversal complete. Processed 13 total variants in 0.0 minutes.
15:47:35.085 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.101 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.101 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.101 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.101 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.101 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.101 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.101 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.101 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.101 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.101 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.101 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.101 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.101 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.102 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.102 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.102 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.102 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.103 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:47:35.105 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf
15:47:35.107 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.107 INFO  ProgressMeter - Starting traversal
15:47:35.107 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.108 INFO  ProgressMeter -             unmapped              0.0                    26        1560000.0
15:47:35.108 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:47:35.108 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.129 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.129 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.129 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.129 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.129 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.129 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.129 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.129 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.129 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.130 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.130 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.130 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.130 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.130 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.130 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.130 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.130 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.131 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_1.vcf
15:47:35.133 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/splitVariants_2.vcf
15:47:35.135 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.135 INFO  ProgressMeter - Starting traversal
15:47:35.135 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.137 INFO  ProgressMeter -             unmapped              0.0                    26        1560000.0
15:47:35.137 INFO  ProgressMeter - Traversal complete. Processed 26 total variants in 0.0 minutes.
15:47:35.137 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.158 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.158 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.158 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.158 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.158 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.159 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.159 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.159 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.159 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.159 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.159 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.159 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.159 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.159 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.159 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.159 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.159 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.161 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/baseVariants.vcf
15:47:35.162 INFO  IntervalArgumentCollection - Processing 16000 bp from intervals
15:47:35.163 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.163 INFO  ProgressMeter - Starting traversal
15:47:35.163 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.164 INFO  ProgressMeter -             unmapped              0.0                    14         Infinity
15:47:35.164 INFO  ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
15:47:35.164 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.185 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.185 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.185 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.185 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.185 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.185 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.185 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.186 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.186 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.186 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.186 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.186 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.186 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.186 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.186 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.186 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.186 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.187 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:47:35.188 INFO  IntervalArgumentCollection - Processing 16000 bp from intervals
15:47:35.189 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.189 INFO  ProgressMeter - Starting traversal
15:47:35.189 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.189 INFO  ProgressMeter -             unmapped              0.0                     7         Infinity
15:47:35.189 INFO  ProgressMeter - Traversal complete. Processed 7 total variants in 0.0 minutes.
15:47:35.189 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.212 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.212 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.212 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.212 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.212 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.212 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.212 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.212 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.212 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.212 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.212 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.212 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.212 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.212 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.213 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.213 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.213 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.214 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:47:35.215 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf
15:47:35.217 INFO  IntervalArgumentCollection - Processing 16000 bp from intervals
15:47:35.217 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.218 INFO  ProgressMeter - Starting traversal
15:47:35.218 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.218 INFO  ProgressMeter -             unmapped              0.0                    14         Infinity
15:47:35.219 INFO  ProgressMeter - Traversal complete. Processed 14 total variants in 0.0 minutes.
15:47:35.219 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240
15:47:35.239 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.239 INFO  TestMultiVariantWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:47:35.239 INFO  TestMultiVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:35.239 INFO  TestMultiVariantWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:47:35.239 INFO  TestMultiVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:47:35.239 INFO  TestMultiVariantWalker - Start Date/Time: May 19, 2025 at 3:47:35 PM GMT
15:47:35.239 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.239 INFO  TestMultiVariantWalker - ------------------------------------------------------------
15:47:35.240 INFO  TestMultiVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:35.240 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:35.240 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:35.240 INFO  TestMultiVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:35.240 INFO  TestMultiVariantWalker - Deflater: IntelDeflater
15:47:35.240 INFO  TestMultiVariantWalker - Inflater: IntelInflater
15:47:35.240 INFO  TestMultiVariantWalker - GCS max retries/reopens: 20
15:47:35.240 INFO  TestMultiVariantWalker - Requester pays: disabled
15:47:35.240 INFO  TestMultiVariantWalker - Initializing engine
15:47:35.241 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_1.vcf
15:47:35.242 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/MultiVariantDataSource/interleavedVariants_2.vcf
15:47:35.244 INFO  IntervalArgumentCollection - Processing 401 bp from intervals
15:47:35.244 INFO  TestMultiVariantWalker - Done initializing engine
15:47:35.244 INFO  ProgressMeter - Starting traversal
15:47:35.244 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
15:47:35.245 INFO  ProgressMeter -             unmapped              0.0                     3         180000.0
15:47:35.245 INFO  ProgressMeter - Traversal complete. Processed 3 total variants in 0.0 minutes.
15:47:35.245 INFO  TestMultiVariantWalker - Shutting down engine
[May 19, 2025 at 3:47:35 PM GMT] org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest$TestMultiVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1562378240