Class org.broadinstitute.hellbender.tools.GetSampleNameIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasicUsage |
0.069s |
passed |
| testMultiSampleBam |
0.080s |
passed |
| testUrlEncoding |
0.067s |
passed |
Standard error
17:39:06.654 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
17:39:06.657 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6093785806691675708.so: /tmp/libgkl_compression6093785806691675708.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:39:06.657 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
17:39:06.660 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1800164545237382252.so: /tmp/libgkl_compression1800164545237382252.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:39:06.661 INFO GetSampleName - ------------------------------------------------------------
17:39:06.662 INFO GetSampleName - org.broadinstitute.hellbender.tools vUnavailable
17:39:06.662 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/
17:39:06.662 INFO GetSampleName - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:39:06.662 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:39:06.662 INFO GetSampleName - Start Date/Time: October 27, 2025 at 5:39:06 PM UTC
17:39:06.662 INFO GetSampleName - ------------------------------------------------------------
17:39:06.662 INFO GetSampleName - ------------------------------------------------------------
17:39:06.662 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:39:06.662 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:39:06.662 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:39:06.662 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:39:06.662 INFO GetSampleName - Deflater: JdkDeflater
17:39:06.662 INFO GetSampleName - Inflater: JdkInflater
17:39:06.662 INFO GetSampleName - GCS max retries/reopens: 20
17:39:06.662 INFO GetSampleName - Requester pays: disabled
17:39:06.662 INFO GetSampleName - Initializing engine
17:39:06.663 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:39:06.663 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:39:06.663 INFO GetSampleName - Done initializing engine
17:39:06.664 INFO ProgressMeter - Starting traversal
17:39:06.664 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:39:06.664 INFO ProgressMeter - unmapped 0.0 0 NaN
17:39:06.664 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:39:06.664 INFO GetSampleName - Shutting down engine
[October 27, 2025 at 5:39:06 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:39:06 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:39:06.806 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
17:39:06.809 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2048981332462215662.so: /tmp/libgkl_compression2048981332462215662.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:39:06.809 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
17:39:06.812 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression16389842562702400698.so: /tmp/libgkl_compression16389842562702400698.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:39:06.813 INFO GetSampleName - ------------------------------------------------------------
17:39:06.813 INFO GetSampleName - org.broadinstitute.hellbender.tools vUnavailable
17:39:06.813 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/
17:39:06.813 INFO GetSampleName - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:39:06.813 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:39:06.813 INFO GetSampleName - Start Date/Time: October 27, 2025 at 5:39:06 PM UTC
17:39:06.813 INFO GetSampleName - ------------------------------------------------------------
17:39:06.813 INFO GetSampleName - ------------------------------------------------------------
17:39:06.813 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:39:06.813 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:39:06.813 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:39:06.813 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:39:06.813 INFO GetSampleName - Deflater: JdkDeflater
17:39:06.813 INFO GetSampleName - Inflater: JdkInflater
17:39:06.813 INFO GetSampleName - GCS max retries/reopens: 20
17:39:06.813 INFO GetSampleName - Requester pays: disabled
17:39:06.813 INFO GetSampleName - Initializing engine
17:39:06.813 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:39:06.813 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:39:06.814 INFO GetSampleName - Done initializing engine
17:39:06.814 INFO ProgressMeter - Starting traversal
17:39:06.814 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:39:06.814 INFO ProgressMeter - unmapped 0.0 0 NaN
17:39:06.814 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:39:06.814 INFO GetSampleName - Shutting down engine
[October 27, 2025 at 5:39:06 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000