Class org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest
Tests
| Test |
Duration |
Result |
| assertThatExpectedOutputUpdateToggleIsDisabled |
0s |
passed |
| testBasic |
0.749s |
passed |
| testBasicBQ |
0.672s |
passed |
Standard error
17:53:12.294 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
17:53:12.297 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression4582980591801605.so: /tmp/local16469784102307886954/libgkl_compression4582980591801605.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:12.297 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
17:53:12.300 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression2221164850482177889.so: /tmp/local16469784102307886954/libgkl_compression2221164850482177889.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:12.301 INFO AddFlowSNVQuality - ------------------------------------------------------------
17:53:12.301 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
17:53:12.301 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
17:53:12.301 INFO AddFlowSNVQuality - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:53:12.301 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:53:12.301 INFO AddFlowSNVQuality - Start Date/Time: October 27, 2025 at 5:53:12 PM UTC
17:53:12.301 INFO AddFlowSNVQuality - ------------------------------------------------------------
17:53:12.301 INFO AddFlowSNVQuality - ------------------------------------------------------------
17:53:12.301 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:53:12.301 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:53:12.301 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:53:12.301 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:53:12.301 INFO AddFlowSNVQuality - Deflater: JdkDeflater
17:53:12.301 INFO AddFlowSNVQuality - Inflater: JdkInflater
17:53:12.301 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
17:53:12.301 INFO AddFlowSNVQuality - Requester pays: disabled
17:53:12.301 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
17:53:12.301 INFO AddFlowSNVQuality - Initializing engine
17:53:12.328 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:53:12.353 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:53:12.354 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:53:12.354 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:53:12.370 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
17:53:12.372 INFO AddFlowSNVQuality - Done initializing engine
17:53:12.384 INFO ProgressMeter - Starting traversal
17:53:12.384 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
17:53:12.907 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
17:53:12.907 INFO ProgressMeter - chr1:14608 0.0 4278 490783.9
17:53:12.907 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
17:53:12.957 INFO AddFlowSNVQuality - Shutting down engine
[October 27, 2025 at 5:53:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1797259264
17:53:13.041 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
17:53:13.044 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression2332857430057814038.so: /tmp/local16469784102307886954/libgkl_compression2332857430057814038.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:13.044 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
17:53:13.047 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression13651927018959832606.so: /tmp/local16469784102307886954/libgkl_compression13651927018959832606.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:53:13.048 INFO AddFlowSNVQuality - ------------------------------------------------------------
17:53:13.048 INFO AddFlowSNVQuality - org.broadinstitute.hellbender.tools.walkers.featuremapping vUnavailable
17:53:13.048 INFO AddFlowSNVQuality - For support and documentation go to https://software.broadinstitute.org/gatk/
17:53:13.048 INFO AddFlowSNVQuality - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:53:13.048 INFO AddFlowSNVQuality - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:53:13.048 INFO AddFlowSNVQuality - Start Date/Time: October 27, 2025 at 5:53:13 PM UTC
17:53:13.048 INFO AddFlowSNVQuality - ------------------------------------------------------------
17:53:13.048 INFO AddFlowSNVQuality - ------------------------------------------------------------
17:53:13.048 INFO AddFlowSNVQuality - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:53:13.048 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:53:13.048 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:53:13.048 INFO AddFlowSNVQuality - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:53:13.048 INFO AddFlowSNVQuality - Deflater: JdkDeflater
17:53:13.048 INFO AddFlowSNVQuality - Inflater: JdkInflater
17:53:13.048 INFO AddFlowSNVQuality - GCS max retries/reopens: 20
17:53:13.048 INFO AddFlowSNVQuality - Requester pays: disabled
17:53:13.048 WARN AddFlowSNVQuality -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: AddFlowSNVQuality is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
17:53:13.048 INFO AddFlowSNVQuality - Initializing engine
17:53:13.074 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:53:13.099 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:53:13.100 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:53:13.100 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:53:13.114 INFO IntervalArgumentCollection - Processing 15000 bp from intervals
17:53:13.117 INFO AddFlowSNVQuality - Done initializing engine
17:53:13.133 INFO ProgressMeter - Starting traversal
17:53:13.133 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
17:53:13.577 INFO AddFlowSNVQuality - 0 read(s) filtered by: WellformedReadFilter
17:53:13.578 INFO ProgressMeter - chr1:14608 0.0 4278 576809.0
17:53:13.578 INFO ProgressMeter - Traversal complete. Processed 4278 total reads in 0.0 minutes.
17:53:13.628 INFO AddFlowSNVQuality - Shutting down engine
[October 27, 2025 at 5:53:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1797259264