Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.150s |
passed |
| testIndelCase |
0.596s |
passed |
Standard error
15:22:09.200 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:22:09.201 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:22:09.201 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 3:22:09 PM GMT
15:22:09.201 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:22:09.201 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:22:09.201 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
15:22:09.201 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:22:09.201 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:22:09.201 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:22:09.201 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
15:22:09.201 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
15:22:09.201 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:22:09.201 INFO ValidateBasicSomaticShortMutations - Initializing engine
15:22:09.209 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
15:22:09.212 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
15:22:09.213 INFO IntervalArgumentCollection - Processing 2 bp from intervals
15:22:09.213 INFO ValidateBasicSomaticShortMutations - Done initializing engine
15:22:09.220 INFO ProgressMeter - Starting traversal
15:22:09.220 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:22:09.257 INFO ProgressMeter - unmapped 0.0 2 3243.2
15:22:09.257 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:22:09.258 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 3:22:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
15:22:09.344 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:22:09.344 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:22:09.344 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
15:22:09.344 INFO ValidateBasicSomaticShortMutations - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:22:09.344 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:22:09.344 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 3:22:09 PM GMT
15:22:09.344 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:22:09.344 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:22:09.344 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:22:09.344 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
15:22:09.344 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
15:22:09.344 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:22:09.344 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:22:09.344 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:22:09.344 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:22:09.345 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
15:22:09.345 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
15:22:09.345 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
15:22:09.345 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
15:22:09.345 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:22:09.345 INFO ValidateBasicSomaticShortMutations - Initializing engine
15:22:09.349 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
15:22:09.352 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
15:22:09.356 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
15:22:09.357 INFO ValidateBasicSomaticShortMutations - Done initializing engine
15:22:09.357 INFO ProgressMeter - Starting traversal
15:22:09.357 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:22:09.830 INFO ProgressMeter - unmapped 0.0 336 42621.6
15:22:09.830 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
15:22:09.838 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 3:22:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000