Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.018s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.023s |
passed |
| testMissingContigForInterval |
0.108s |
passed |
| testReadFilterOff |
0.022s |
passed |
| testReadFilterOn |
0.023s |
passed |
| testRequiresIndexForInterval |
0.098s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.098s |
passed |
Standard error
[May 27, 2025 at 1:51:21 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
13:51:21.283 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:51:21.284 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
13:51:21.284 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
13:51:21.284 INFO TestGATKToolWithFeatures - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
13:51:21.284 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
13:51:21.284 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 1:51:21 PM GMT
13:51:21.284 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:51:21.284 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:51:21.284 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:51:21.284 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:51:21.284 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:51:21.284 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:51:21.284 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
13:51:21.284 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
13:51:21.284 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
13:51:21.284 INFO TestGATKToolWithFeatures - Requester pays: disabled
13:51:21.284 INFO TestGATKToolWithFeatures - Initializing engine
13:51:21.287 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
13:51:21.288 INFO TestGATKToolWithFeatures - Done initializing engine
13:51:21.288 INFO ProgressMeter - Starting traversal
13:51:21.288 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:51:21.289 INFO ProgressMeter - unmapped 0.0 2 120000.0
13:51:21.289 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
13:51:21.289 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 1:51:21 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
13:51:21.308 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:51:21.308 INFO TestGATKToolWithFeatures - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
13:51:21.308 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
13:51:21.308 INFO TestGATKToolWithFeatures - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
13:51:21.308 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
13:51:21.308 INFO TestGATKToolWithFeatures - Start Date/Time: May 27, 2025 at 1:51:21 PM GMT
13:51:21.308 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:51:21.308 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
13:51:21.308 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:51:21.308 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:51:21.308 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:51:21.308 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:51:21.309 INFO TestGATKToolWithFeatures - Deflater: IntelDeflater
13:51:21.309 INFO TestGATKToolWithFeatures - Inflater: IntelInflater
13:51:21.309 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
13:51:21.309 INFO TestGATKToolWithFeatures - Requester pays: disabled
13:51:21.309 INFO TestGATKToolWithFeatures - Initializing engine
13:51:21.310 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
13:51:21.311 INFO TestGATKToolWithFeatures - Done initializing engine
13:51:21.311 INFO ProgressMeter - Starting traversal
13:51:21.311 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:51:21.313 INFO ProgressMeter - unmapped 0.0 2 60000.0
13:51:21.313 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
13:51:21.313 INFO TestGATKToolWithFeatures - Shutting down engine
[May 27, 2025 at 1:51:21 PM GMT] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 1:51:21 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 1:51:21 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000