Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.176s |
passed |
| testIndelCase |
0.726s |
passed |
Standard error
21:10:45.760 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
21:10:45.760 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:10:45.760 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
21:10:45.760 INFO ValidateBasicSomaticShortMutations - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:10:45.760 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:10:45.760 INFO ValidateBasicSomaticShortMutations - Start Date/Time: June 12, 2025 at 9:10:45 PM GMT
21:10:45.760 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
21:10:45.760 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
21:10:45.760 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: 4.2.0
21:10:45.760 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
21:10:45.760 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
21:10:45.760 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:10:45.760 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:10:45.760 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:10:45.760 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:10:45.760 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
21:10:45.760 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
21:10:45.760 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
21:10:45.760 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
21:10:45.760 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
21:10:45.761 INFO ValidateBasicSomaticShortMutations - Initializing engine
21:10:45.768 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf
21:10:45.772 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf
21:10:45.773 INFO IntervalArgumentCollection - Processing 2 bp from intervals
21:10:45.773 INFO ValidateBasicSomaticShortMutations - Done initializing engine
21:10:45.780 INFO ProgressMeter - Starting traversal
21:10:45.780 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
21:10:45.843 INFO ProgressMeter - unmapped 0.0 2 1904.8
21:10:45.844 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
21:10:45.845 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[June 12, 2025 at 9:10:45 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
21:10:45.976 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
21:10:45.977 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:10:45.977 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Start Date/Time: June 12, 2025 at 9:10:45 PM GMT
21:10:45.977 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
21:10:45.977 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
21:10:45.977 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: 4.2.0
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
21:10:45.977 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:10:45.977 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:10:45.977 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:10:45.977 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
21:10:45.977 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
21:10:45.977 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
21:10:45.977 INFO ValidateBasicSomaticShortMutations - Initializing engine
21:10:45.981 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf
21:10:45.984 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf
21:10:45.989 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
21:10:45.989 INFO ValidateBasicSomaticShortMutations - Done initializing engine
21:10:45.989 INFO ProgressMeter - Starting traversal
21:10:45.989 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
21:10:46.549 INFO ProgressMeter - unmapped 0.0 336 36000.0
21:10:46.550 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
21:10:46.556 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[June 12, 2025 at 9:10:46 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1059061760