Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.149s |
passed |
| testIndelCase |
0.674s |
passed |
Standard error
16:12:02.293 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:12:02.293 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:12:02.293 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:02.293 INFO ValidateBasicSomaticShortMutations - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:12:02.293 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:02.293 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 19, 2025 at 4:12:02 PM GMT
16:12:02.294 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:12:02.294 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:12:02.294 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:12:02.294 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
16:12:02.294 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
16:12:02.294 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:02.294 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:02.294 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:02.294 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:02.294 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
16:12:02.294 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
16:12:02.294 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
16:12:02.294 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
16:12:02.294 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:12:02.294 INFO ValidateBasicSomaticShortMutations - Initializing engine
16:12:02.301 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
16:12:02.304 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
16:12:02.305 INFO IntervalArgumentCollection - Processing 2 bp from intervals
16:12:02.306 INFO ValidateBasicSomaticShortMutations - Done initializing engine
16:12:02.309 INFO ProgressMeter - Starting traversal
16:12:02.309 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:12:02.348 INFO ProgressMeter - unmapped 0.0 2 3076.9
16:12:02.348 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
16:12:02.349 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 19, 2025 at 4:12:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
16:12:02.446 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:12:02.446 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:12:02.446 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 19, 2025 at 4:12:02 PM GMT
16:12:02.447 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:12:02.447 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:12:02.447 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
16:12:02.447 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:12:02.447 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:12:02.447 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:12:02.447 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
16:12:02.447 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
16:12:02.447 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:12:02.447 INFO ValidateBasicSomaticShortMutations - Initializing engine
16:12:02.452 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
16:12:02.455 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
16:12:02.459 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
16:12:02.459 INFO ValidateBasicSomaticShortMutations - Done initializing engine
16:12:02.459 INFO ProgressMeter - Starting traversal
16:12:02.459 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:12:03.001 INFO ProgressMeter - unmapped 0.0 336 37195.6
16:12:03.001 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
16:12:03.008 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 19, 2025 at 4:12:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000