Class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest

all > org.broadinstitute.hellbender.cmdline.GATKPlugin > GATKAnnotationPluginDescriptorUnitTest

tests

failures

ignored

2.906s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testAnnotationArguments	0.033s	passed
testAnnotationGroupAdditive	0.016s	passed
testConfigFileControlsAnnotationPackages	2.110s	passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1)	0.018s	passed
testGetAllowedValuesForDescriptorHelpGroups	0.014s	passed
testGetAllowedValuesForDescriptorHelp[0]([])	0.016s	passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@79fbcef4])	0.014s	passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@198a653, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@3119fcad])	0.015s	passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@299f9a81, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@4b19ee18])	0.020s	passed
testGetClassForPluginHelpFromReflection	0.013s	passed
testGetDefaultInstances	0.014s	passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@279e4506, false, false)	0.019s	passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@4b02dc4e, true, true)	0.018s	passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@328b2c2a, true, false)	0.016s	passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@60515ab1, true, true)	0.013s	passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@1d0f03f6, true, true)	0.024s	passed
testHierarchicalAnnotationDiscovery	0.002s	passed
testIncludeAllExcludeIndividual	0.038s	passed
testIncludeDefaultExcludeIndividual	0.013s	passed
testIncludeDefaultGroupExcludeIndividual	0.012s	passed
testIncludeUserGroupExcludeIndividual	0.012s	passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0.012s	passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation])	0.012s	passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object])	0.019s	passed
testInvalidToolDefaultAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0.001s	passed
testInvalidToolDefaultAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation])	0s	passed
testInvalidToolDefaultAnnotationGroups[2]([class java.lang.Object])	0s	passed
testInvalidUserSpecifiedAnnotations[0]([-A, StandardAnnotation])	0.012s	passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality])	0.011s	passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality])	0.012s	passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality])	0.013s	passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo])	0.012s	passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator])	0.011s	passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@36b2b6e6, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@5a9004e1], [Ljava.lang.String;@17af9f67, true, 5, 0)	0.012s	passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@6c4a1980, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@2125086c, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@65c634f2], [Ljava.lang.String;@57f9f387, true, 5, -0.3333)	0.013s	passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@530aa75c, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@593d0173, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@4a0a93ce], [Ljava.lang.String;@64404db6, false, 0, 0)	0.017s	passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@c725dfa, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@3a8cc099, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@756b703d], [Ljava.lang.String;@1c00a9f0, true, 5, -0.2941)	0.013s	passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@18ada4e1, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@10cf3e4f, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@359f3401], [Ljava.lang.String;@242a3997, false, 0, -0.3333)	0.015s	passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@52b2713a, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@54e39504, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2bdf6c7c], [Ljava.lang.String;@13ac1657, false, 0, -0.3333)	0.017s	passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@6812708d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@7a4c1a6c, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@123a21ad], [Ljava.lang.String;@51179fad, true, 5, -0.2941)	0.015s	passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@74e111a8], [Ljava.lang.String;@6e6ec9c, false, 0, -0.2941)	0.019s	passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@f6b128b], [Ljava.lang.String;@470fc16c, false, 0, 0)	0.014s	passed
testNoAnnotations	0.012s	passed
testOverridingInstancesWithGetInstance	0.001s	passed
testPossibleDeNovoAnnotationArguments	0.031s	passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine	0.054s	passed
testUseAllAnnotations	0.055s	passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns	0.053s	passed

Standard error

19:01:37.035 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-0192957-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
19:01:37.132 INFO  TestAnnotationsTool - ------------------------------------------------------------
19:01:37.135 INFO  TestAnnotationsTool - The Genome Analysis Toolkit (GATK) v0192957-SNAPSHOT
19:01:37.135 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
19:01:37.135 INFO  TestAnnotationsTool - Executing as root@41e59f58627b on Linux v6.11.0-1014-azure amd64
19:01:37.135 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:01:37.135 INFO  TestAnnotationsTool - Start Date/Time: May 19, 2025 at 7:01:36 PM GMT
19:01:37.135 INFO  TestAnnotationsTool - ------------------------------------------------------------
19:01:37.135 INFO  TestAnnotationsTool - ------------------------------------------------------------
19:01:37.138 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:01:37.138 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:01:37.139 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:01:37.139 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:01:37.139 INFO  TestAnnotationsTool - Deflater: IntelDeflater
19:01:37.139 INFO  TestAnnotationsTool - Inflater: IntelInflater
19:01:37.139 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
19:01:37.139 INFO  TestAnnotationsTool - Requester pays: disabled
19:01:37.140 INFO  TestAnnotationsTool - Initializing engine
19:01:37.235 INFO  TestAnnotationsTool - Done initializing engine
19:01:37.236 INFO  ProgressMeter - Starting traversal
19:01:37.237 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
19:01:37.239 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
19:01:37.240 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:01:37.240 INFO  TestAnnotationsTool - Shutting down engine
[May 19, 2025 at 7:01:37 PM GMT] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=188743680
19:01:37.532 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
19:01:37.570 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
19:01:37.583 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
19:01:37.777 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
19:01:37.827 INFO  PedReader - Phenotype is other? false
19:01:37.828 INFO  PedReader - Phenotype is other? false
19:01:37.842 INFO  PedReader - Phenotype is other? false
19:01:37.842 INFO  PedReader - Phenotype is other? false
19:01:37.843 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
19:01:37.941 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
19:01:37.941 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default