Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.199s |
passed |
| testIndelCase |
0.873s |
passed |
Standard error
18:42:52.912 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:42:52.912 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:42:52.912 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
18:42:52.912 INFO ValidateBasicSomaticShortMutations - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:42:52.912 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:42:52.913 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 6:42:52 PM GMT
18:42:52.913 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:42:52.913 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:42:52.913 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:42:52.913 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
18:42:52.913 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
18:42:52.913 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:42:52.913 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:42:52.913 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:42:52.913 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:42:52.913 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
18:42:52.913 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
18:42:52.913 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
18:42:52.913 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
18:42:52.913 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:42:52.914 INFO ValidateBasicSomaticShortMutations - Initializing engine
18:42:52.925 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
18:42:52.929 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
18:42:52.931 INFO IntervalArgumentCollection - Processing 2 bp from intervals
18:42:52.931 INFO ValidateBasicSomaticShortMutations - Done initializing engine
18:42:52.937 INFO ProgressMeter - Starting traversal
18:42:52.938 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:42:52.994 INFO ProgressMeter - unmapped 0.0 2 2142.9
18:42:52.994 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
18:42:52.996 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 6:42:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
18:42:53.157 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:42:53.157 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:42:53.157 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 6:42:53 PM GMT
18:42:53.158 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:42:53.158 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:42:53.158 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
18:42:53.158 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:42:53.158 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:42:53.158 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:42:53.158 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
18:42:53.158 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
18:42:53.158 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:42:53.158 INFO ValidateBasicSomaticShortMutations - Initializing engine
18:42:53.163 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
18:42:53.167 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
18:42:53.171 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
18:42:53.172 INFO ValidateBasicSomaticShortMutations - Done initializing engine
18:42:53.172 INFO ProgressMeter - Starting traversal
18:42:53.172 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:42:53.847 INFO ProgressMeter - unmapped 0.0 336 29866.7
18:42:53.848 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
18:42:53.854 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 6:42:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600