Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest
Tests
| Test |
Duration |
Result |
| testCountBasesInReferenceFull |
0.050s |
passed |
| testCountBasesInReferenceWithInterval |
0.013s |
passed |
| testCountBasesInReferenceWithOutputFile |
0.019s |
passed |
Standard output
A : 4546
C : 4995
G : 4559
N : 46000
T : 3900
N : 1001
A : 4546
C : 4995
G : 4559
N : 46000
T : 3900
Standard error
17:53:10.077 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
17:53:10.080 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression17185325939053552874.so: /tmp/local16469784102307886954/libgkl_compression17185325939053552874.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:10.080 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
17:53:10.084 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression18040036263526754639.so: /tmp/local16469784102307886954/libgkl_compression18040036263526754639.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:10.085 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.085 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
17:53:10.085 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
17:53:10.085 INFO CountBasesInReference - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:53:10.085 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:53:10.085 INFO CountBasesInReference - Start Date/Time: October 27, 2025 at 5:53:10 PM UTC
17:53:10.085 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.085 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.085 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:53:10.085 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:53:10.085 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:53:10.085 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:53:10.085 INFO CountBasesInReference - Deflater: JdkDeflater
17:53:10.085 INFO CountBasesInReference - Inflater: JdkInflater
17:53:10.085 INFO CountBasesInReference - GCS max retries/reopens: 20
17:53:10.085 INFO CountBasesInReference - Requester pays: disabled
17:53:10.085 INFO CountBasesInReference - Initializing engine
17:53:10.086 INFO CountBasesInReference - Done initializing engine
17:53:10.086 INFO ProgressMeter - Starting traversal
17:53:10.086 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
17:53:10.122 INFO ProgressMeter - 4:16000 0.0 64000 106666666.7
17:53:10.123 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
17:53:10.123 INFO CountBasesInReference - Shutting down engine
[October 27, 2025 at 5:53:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1797259264
17:53:10.127 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
17:53:10.130 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression9206323043796298192.so: /tmp/local16469784102307886954/libgkl_compression9206323043796298192.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:10.130 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
17:53:10.133 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression1500399183706009579.so: /tmp/local16469784102307886954/libgkl_compression1500399183706009579.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:10.134 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.134 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
17:53:10.134 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
17:53:10.134 INFO CountBasesInReference - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:53:10.134 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:53:10.134 INFO CountBasesInReference - Start Date/Time: October 27, 2025 at 5:53:10 PM UTC
17:53:10.134 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.134 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.134 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:53:10.134 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:53:10.134 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:53:10.134 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:53:10.134 INFO CountBasesInReference - Deflater: JdkDeflater
17:53:10.134 INFO CountBasesInReference - Inflater: JdkInflater
17:53:10.134 INFO CountBasesInReference - GCS max retries/reopens: 20
17:53:10.134 INFO CountBasesInReference - Requester pays: disabled
17:53:10.134 INFO CountBasesInReference - Initializing engine
17:53:10.135 INFO IntervalArgumentCollection - Processing 1001 bp from intervals
17:53:10.135 INFO CountBasesInReference - Done initializing engine
17:53:10.135 INFO ProgressMeter - Starting traversal
17:53:10.135 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
17:53:10.135 INFO ProgressMeter - 1:5999 0.0 1001 Infinity
17:53:10.135 INFO ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
17:53:10.135 INFO CountBasesInReference - Shutting down engine
[October 27, 2025 at 5:53:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1797259264
17:53:10.140 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
17:53:10.142 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression13469076284531845301.so: /tmp/local16469784102307886954/libgkl_compression13469076284531845301.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:10.143 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
17:53:10.145 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression2754207839936082118.so: /tmp/local16469784102307886954/libgkl_compression2754207839936082118.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:10.146 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.146 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
17:53:10.146 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
17:53:10.146 INFO CountBasesInReference - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:53:10.146 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:53:10.146 INFO CountBasesInReference - Start Date/Time: October 27, 2025 at 5:53:10 PM UTC
17:53:10.146 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.146 INFO CountBasesInReference - ------------------------------------------------------------
17:53:10.146 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:53:10.146 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:53:10.146 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:53:10.146 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:53:10.147 INFO CountBasesInReference - Deflater: JdkDeflater
17:53:10.147 INFO CountBasesInReference - Inflater: JdkInflater
17:53:10.147 INFO CountBasesInReference - GCS max retries/reopens: 20
17:53:10.147 INFO CountBasesInReference - Requester pays: disabled
17:53:10.147 INFO CountBasesInReference - Initializing engine
17:53:10.147 INFO CountBasesInReference - Done initializing engine
17:53:10.147 INFO ProgressMeter - Starting traversal
17:53:10.147 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
17:53:10.154 INFO ProgressMeter - 4:16000 0.0 64000 548571428.6
17:53:10.154 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
17:53:10.155 INFO CountBasesInReference - Shutting down engine
[October 27, 2025 at 5:53:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1797259264