Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.129s |
passed |
| testIndelCase |
0.816s |
passed |
Standard error
19:09:22.280 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:09:22.280 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
19:09:22.280 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:22.280 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:09:22.280 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:09:22.280 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 19, 2025 at 7:09:22 PM UTC
19:09:22.280 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:09:22.280 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:09:22.280 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:22.280 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:22.280 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:22.281 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:22.281 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
19:09:22.281 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
19:09:22.281 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
19:09:22.281 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
19:09:22.281 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:09:22.281 INFO ValidateBasicSomaticShortMutations - Initializing engine
19:09:22.286 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf
19:09:22.289 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf
19:09:22.290 INFO IntervalArgumentCollection - Processing 2 bp from intervals
19:09:22.290 INFO ValidateBasicSomaticShortMutations - Done initializing engine
19:09:22.293 INFO ProgressMeter - Starting traversal
19:09:22.293 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:09:22.342 INFO ProgressMeter - unmapped 0.0 2 2449.0
19:09:22.342 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
19:09:22.343 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 19, 2025 at 7:09:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
19:09:22.411 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:09:22.411 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
19:09:22.411 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:22.411 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:09:22.411 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:09:22.411 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 19, 2025 at 7:09:22 PM UTC
19:09:22.411 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:09:22.411 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
19:09:22.411 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:22.411 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:22.411 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:22.411 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:22.412 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
19:09:22.412 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
19:09:22.412 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
19:09:22.412 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
19:09:22.412 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
19:09:22.412 INFO ValidateBasicSomaticShortMutations - Initializing engine
19:09:22.416 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf
19:09:22.418 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf
19:09:22.423 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
19:09:22.423 INFO ValidateBasicSomaticShortMutations - Done initializing engine
19:09:22.423 INFO ProgressMeter - Starting traversal
19:09:22.423 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:09:23.140 INFO ProgressMeter - unmapped 0.0 336 28117.2
19:09:23.140 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
19:09:23.146 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 19, 2025 at 7:09:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1497366528