Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.122s |
passed |
| testIndelCase |
0.686s |
passed |
Standard error
17:57:57.867 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
17:57:57.870 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13262240230548254293.so: /tmp/libgkl_compression13262240230548254293.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:57:57.870 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
17:57:57.873 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6826654217134298026.so: /tmp/libgkl_compression6826654217134298026.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:57:57.874 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
17:57:57.874 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
17:57:57.874 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
17:57:57.874 INFO ValidateBasicSomaticShortMutations - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:57:57.874 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:57:57.874 INFO ValidateBasicSomaticShortMutations - Start Date/Time: October 27, 2025 at 5:57:57 PM UTC
17:57:57.874 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
17:57:57.874 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
17:57:57.875 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:57:57.875 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:57:57.875 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:57:57.875 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:57:57.875 INFO ValidateBasicSomaticShortMutations - Deflater: JdkDeflater
17:57:57.875 INFO ValidateBasicSomaticShortMutations - Inflater: JdkInflater
17:57:57.875 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
17:57:57.875 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
17:57:57.875 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
17:57:57.875 INFO ValidateBasicSomaticShortMutations - Initializing engine
17:57:57.876 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:57:57.876 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:57:57.877 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:57:57.877 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:57:57.881 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf
17:57:57.884 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf
17:57:57.885 INFO IntervalArgumentCollection - Processing 2 bp from intervals
17:57:57.885 INFO ValidateBasicSomaticShortMutations - Done initializing engine
17:57:57.888 INFO ProgressMeter - Starting traversal
17:57:57.888 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
17:57:57.928 INFO ProgressMeter - unmapped 0.0 2 3000.0
17:57:57.928 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
17:57:57.929 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[October 27, 2025 at 5:57:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1690304512
17:57:57.990 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
17:57:57.993 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression5081348794521134484.so: /tmp/libgkl_compression5081348794521134484.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:57:57.993 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
17:57:57.996 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6237598294157585617.so: /tmp/libgkl_compression6237598294157585617.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:57:57.997 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
17:57:57.997 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
17:57:57.997 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
17:57:57.997 INFO ValidateBasicSomaticShortMutations - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:57:57.997 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:57:57.997 INFO ValidateBasicSomaticShortMutations - Start Date/Time: October 27, 2025 at 5:57:57 PM UTC
17:57:57.997 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
17:57:57.997 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
17:57:57.997 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:57:57.997 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:57:57.997 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:57:57.997 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:57:57.997 INFO ValidateBasicSomaticShortMutations - Deflater: JdkDeflater
17:57:57.997 INFO ValidateBasicSomaticShortMutations - Inflater: JdkInflater
17:57:57.997 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
17:57:57.997 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
17:57:57.997 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
17:57:57.997 INFO ValidateBasicSomaticShortMutations - Initializing engine
17:57:57.998 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:57:57.999 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:57:57.999 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:57:57.999 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:57:58.001 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf
17:57:58.004 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf
17:57:58.006 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
17:57:58.006 INFO ValidateBasicSomaticShortMutations - Done initializing engine
17:57:58.006 INFO ProgressMeter - Starting traversal
17:57:58.006 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
17:57:58.604 INFO ProgressMeter - unmapped 0.0 336 33712.4
17:57:58.604 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
17:57:58.607 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[October 27, 2025 at 5:57:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1677721600