Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.157s |
passed |
| testIndelCase |
0.841s |
passed |
Standard error
14:45:51.731 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:45:51.731 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:45:51.731 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
14:45:51.731 INFO ValidateBasicSomaticShortMutations - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:45:51.731 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:45:51.731 INFO ValidateBasicSomaticShortMutations - Start Date/Time: June 2, 2025 at 2:45:51 PM GMT
14:45:51.731 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:45:51.731 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:45:51.731 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:45:51.731 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
14:45:51.731 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
14:45:51.731 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:45:51.731 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:45:51.731 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:45:51.732 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:45:51.732 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
14:45:51.732 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
14:45:51.732 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
14:45:51.732 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
14:45:51.732 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:45:51.732 INFO ValidateBasicSomaticShortMutations - Initializing engine
14:45:51.740 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
14:45:51.743 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
14:45:51.744 INFO IntervalArgumentCollection - Processing 2 bp from intervals
14:45:51.744 INFO ValidateBasicSomaticShortMutations - Done initializing engine
14:45:51.749 INFO ProgressMeter - Starting traversal
14:45:51.749 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
14:45:51.803 INFO ProgressMeter - unmapped 0.0 2 2264.2
14:45:51.803 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:45:51.804 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[June 2, 2025 at 2:45:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
14:45:51.934 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:45:51.934 INFO ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:45:51.934 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
14:45:51.934 INFO ValidateBasicSomaticShortMutations - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:45:51.934 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:45:51.934 INFO ValidateBasicSomaticShortMutations - Start Date/Time: June 2, 2025 at 2:45:51 PM GMT
14:45:51.934 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:45:51.934 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:45:51.934 INFO ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:45:51.934 INFO ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
14:45:51.934 INFO ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
14:45:51.934 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:45:51.935 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:45:51.935 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:45:51.935 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:45:51.935 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
14:45:51.935 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
14:45:51.935 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
14:45:51.935 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
14:45:51.935 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:45:51.935 INFO ValidateBasicSomaticShortMutations - Initializing engine
14:45:51.939 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
14:45:51.943 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
14:45:51.947 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
14:45:51.948 INFO ValidateBasicSomaticShortMutations - Done initializing engine
14:45:51.948 INFO ProgressMeter - Starting traversal
14:45:51.948 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
14:45:52.622 INFO ProgressMeter - unmapped 0.0 336 29955.4
14:45:52.622 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
14:45:52.629 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[June 2, 2025 at 2:45:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000