Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.179s |
passed |
| testIndelCase |
0.865s |
passed |
Standard error
19:23:59.138 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:23:59.138 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:23:59.138 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
19:23:59.138 INFO ValidateBasicSomaticShortMutations - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:23:59.138 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:23:59.138 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 19, 2025 at 7:23:59 PM GMT
19:23:59.138 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:23:59.138 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:23:59.139 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:23:59.139 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
19:23:59.139 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
19:23:59.139 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:23:59.139 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:23:59.139 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:23:59.139 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:23:59.139 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
19:23:59.139 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
19:23:59.139 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
19:23:59.139 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
19:23:59.139 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:23:59.139 INFO ValidateBasicSomaticShortMutations - Initializing engine
19:23:59.147 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
19:23:59.151 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
19:23:59.152 INFO IntervalArgumentCollection - Processing 2 bp from intervals
19:23:59.152 INFO ValidateBasicSomaticShortMutations - Done initializing engine
19:23:59.158 INFO ProgressMeter - Starting traversal
19:23:59.159 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:23:59.222 INFO ProgressMeter - unmapped 0.0 2 1904.8
19:23:59.222 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
19:23:59.224 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 19, 2025 at 7:23:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
19:23:59.353 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:23:59.353 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:23:59.353 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
19:23:59.353 INFO ValidateBasicSomaticShortMutations - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:23:59.353 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:23:59.353 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 19, 2025 at 7:23:59 PM GMT
19:23:59.353 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:23:59.353 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:23:59.353 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:23:59.353 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
19:23:59.353 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
19:23:59.353 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:23:59.353 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:23:59.353 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:23:59.354 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:23:59.354 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
19:23:59.354 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
19:23:59.354 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
19:23:59.354 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
19:23:59.354 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:23:59.354 INFO ValidateBasicSomaticShortMutations - Initializing engine
19:23:59.358 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
19:23:59.361 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
19:23:59.365 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
19:23:59.365 INFO ValidateBasicSomaticShortMutations - Done initializing engine
19:23:59.366 INFO ProgressMeter - Starting traversal
19:23:59.366 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:24:00.066 INFO ProgressMeter - unmapped 0.0 336 28800.0
19:24:00.066 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
19:24:00.073 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 19, 2025 at 7:24:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000