Class org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest
Tests
| Test |
Duration |
Result |
| testBestSequenceDictionary_FromVariantIndex |
0.008s |
passed |
| testBestSequenceDictionary_FromVariantReference |
0.008s |
passed |
| testMissingContigForInterval |
0.085s |
passed |
| testReadFilterOff |
0.018s |
passed |
| testReadFilterOn |
0.019s |
passed |
| testRequiresIndexForInterval |
0.072s |
passed |
| testRequiresSequenceDictionaryForInterval |
0.071s |
passed |
Standard error
[October 27, 2025 at 5:38:42 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:38:42.157 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:38:42.160 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression3766132888786660572.so: /tmp/libgkl_compression3766132888786660572.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:38:42.161 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:38:42.164 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression16375721946443364372.so: /tmp/libgkl_compression16375721946443364372.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:38:42.165 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:38:42.165 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
17:38:42.165 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
17:38:42.165 INFO TestGATKToolWithFeatures - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:38:42.165 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:38:42.165 INFO TestGATKToolWithFeatures - Start Date/Time: October 27, 2025 at 5:38:42 PM UTC
17:38:42.165 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:38:42.165 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:38:42.166 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:38:42.166 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:38:42.166 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:38:42.166 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:38:42.166 INFO TestGATKToolWithFeatures - Deflater: JdkDeflater
17:38:42.166 INFO TestGATKToolWithFeatures - Inflater: JdkInflater
17:38:42.166 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
17:38:42.166 INFO TestGATKToolWithFeatures - Requester pays: disabled
17:38:42.166 INFO TestGATKToolWithFeatures - Initializing engine
17:38:42.167 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:38:42.167 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:38:42.168 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
17:38:42.169 INFO TestGATKToolWithFeatures - Done initializing engine
17:38:42.169 INFO ProgressMeter - Starting traversal
17:38:42.169 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
17:38:42.171 INFO ProgressMeter - unmapped 0.0 2 120000.0
17:38:42.171 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
17:38:42.171 INFO TestGATKToolWithFeatures - Shutting down engine
[October 27, 2025 at 5:38:42 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:38:42.176 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:38:42.179 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7517415496634240249.so: /tmp/libgkl_compression7517415496634240249.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:38:42.179 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:38:42.182 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9495822458934681716.so: /tmp/libgkl_compression9495822458934681716.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:38:42.184 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:38:42.184 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
17:38:42.184 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
17:38:42.184 INFO TestGATKToolWithFeatures - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:38:42.184 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:38:42.184 INFO TestGATKToolWithFeatures - Start Date/Time: October 27, 2025 at 5:38:42 PM UTC
17:38:42.184 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:38:42.184 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:38:42.184 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:38:42.184 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:38:42.184 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:38:42.184 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:38:42.184 INFO TestGATKToolWithFeatures - Deflater: JdkDeflater
17:38:42.185 INFO TestGATKToolWithFeatures - Inflater: JdkInflater
17:38:42.185 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
17:38:42.185 INFO TestGATKToolWithFeatures - Requester pays: disabled
17:38:42.185 INFO TestGATKToolWithFeatures - Initializing engine
17:38:42.185 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:38:42.185 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:38:42.186 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/VariantWalkerTest_VariantsWithReads.vcf
17:38:42.187 INFO TestGATKToolWithFeatures - Done initializing engine
17:38:42.187 INFO ProgressMeter - Starting traversal
17:38:42.187 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
17:38:42.189 INFO ProgressMeter - unmapped 0.0 2 60000.0
17:38:42.189 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
17:38:42.190 INFO TestGATKToolWithFeatures - Shutting down engine
[October 27, 2025 at 5:38:42 PM UTC] org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:38:42 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:38:42 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000