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

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

tests

failures

ignored

2.039s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testAnnotationArguments	0.028s	passed
testAnnotationGroupAdditive	0.005s	passed
testConfigFileControlsAnnotationPackages	1.868s	passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1)	0.005s	passed
testGetAllowedValuesForDescriptorHelpGroups	0.003s	passed
testGetAllowedValuesForDescriptorHelp[0]([])	0.004s	passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@3d57fb9e])	0.004s	passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@5a9051fd, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7614378d])	0.003s	passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5f8df69, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@1ce6a9bd])	0.003s	passed
testGetClassForPluginHelpFromReflection	0.002s	passed
testGetDefaultInstances	0.003s	passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@111cbcda, false, false)	0.003s	passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@3d9c8c3c, true, true)	0.003s	passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@3636f2a7, true, false)	0.003s	passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@30b9728f, true, true)	0.004s	passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@b842275, true, true)	0.003s	passed
testHierarchicalAnnotationDiscovery	0.002s	passed
testIncludeAllExcludeIndividual	0.010s	passed
testIncludeDefaultExcludeIndividual	0.002s	passed
testIncludeDefaultGroupExcludeIndividual	0.004s	passed
testIncludeUserGroupExcludeIndividual	0.003s	passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0.003s	passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation])	0.002s	passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object])	0.002s	passed
testInvalidToolDefaultAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0s	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])	0.003s	passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality])	0.003s	passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality])	0.002s	passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality])	0.002s	passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo])	0.002s	passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator])	0.002s	passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@1b7a4930, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@591a4d25], [Ljava.lang.String;@4bfe83d, true, 5, 0)	0.002s	passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@5d77be8e, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@55a055cc, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@1ab1d93d], [Ljava.lang.String;@57167ccb, true, 5, -0.3333)	0.004s	passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@c89e263, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4d5ea776, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5d68be4f], [Ljava.lang.String;@34eb5d01, false, 0, 0)	0.003s	passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@29db008c, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@1d008e61, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@191b44ca], [Ljava.lang.String;@5de243bb, true, 5, -0.2941)	0.004s	passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@67c2b55d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@5db04bd2, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6f921e32], [Ljava.lang.String;@31c5304f, false, 0, -0.3333)	0.003s	passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@63d66761, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@434a8938, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@237cd264], [Ljava.lang.String;@51cd2d2, false, 0, -0.3333)	0.006s	passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@195cbf5e, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4cb82b09, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@49665f92], [Ljava.lang.String;@b68932b, true, 5, -0.2941)	0.003s	passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6c19769c], [Ljava.lang.String;@434d001d, false, 0, -0.2941)	0.006s	passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@443dae2], [Ljava.lang.String;@8f09a02, false, 0, 0)	0.004s	passed
testNoAnnotations	0.002s	passed
testOverridingInstancesWithGetInstance	0.001s	passed
testPossibleDeNovoAnnotationArguments	0.002s	passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine	0.005s	passed
testUseAllAnnotations	0.004s	passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns	0.004s	passed

Standard error

18:45:48.083 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.8.11/13f95ee601084b8bf047b2a37f6ea36cd588b96b/gkl-0.8.11.jar!/com/intel/gkl/native/libgkl_compression.so
18:45:48.194 INFO  TestAnnotationsTool - ------------------------------------------------------------
18:45:48.196 INFO  TestAnnotationsTool - org.broadinstitute.hellbender.cmdline.GATKPlugin vUnavailable
18:45:48.197 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
18:45:48.197 INFO  TestAnnotationsTool - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:45:48.197 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:45:48.197 INFO  TestAnnotationsTool - Start Date/Time: May 19, 2025 at 6:45:48 PM UTC
18:45:48.197 INFO  TestAnnotationsTool - ------------------------------------------------------------
18:45:48.197 INFO  TestAnnotationsTool - ------------------------------------------------------------
18:45:48.200 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:45:48.201 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:45:48.201 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:45:48.201 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:45:48.201 INFO  TestAnnotationsTool - Deflater: IntelDeflater
18:45:48.201 INFO  TestAnnotationsTool - Inflater: IntelInflater
18:45:48.201 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
18:45:48.202 INFO  TestAnnotationsTool - Requester pays: disabled
18:45:48.202 INFO  TestAnnotationsTool - Initializing engine
18:45:48.247 INFO  TestAnnotationsTool - Done initializing engine
18:45:48.248 INFO  ProgressMeter - Starting traversal
18:45:48.248 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
18:45:48.251 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
18:45:48.251 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
18:45:48.252 INFO  TestAnnotationsTool - Shutting down engine
[May 19, 2025 at 6:45:48 PM UTC] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=146800640
18:45:48.372 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
18:45:48.380 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
18:45:48.383 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
18:45:48.427 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
18:45:48.441 INFO  PedReader - Phenotype is other? false
18:45:48.442 INFO  PedReader - Phenotype is other? false
18:45:48.445 INFO  PedReader - Phenotype is other? false
18:45:48.446 INFO  PedReader - Phenotype is other? false
18:45:48.446 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
18:45:48.456 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
18:45:48.457 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default