Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.115s |
passed |
| testIndelCase |
0.646s |
passed |
Standard error
16:45:15.408 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:45:15.409 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
16:45:15.409 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
16:45:15.409 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
16:45:15.409 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
16:45:15.409 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 4:45:15 PM UTC
16:45:15.409 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:45:15.409 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:45:15.409 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:45:15.409 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:45:15.409 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:45:15.409 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:45:15.409 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
16:45:15.409 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
16:45:15.409 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
16:45:15.409 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
16:45:15.409 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:45:15.409 INFO ValidateBasicSomaticShortMutations - Initializing engine
16:45:15.415 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
16:45:15.417 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
16:45:15.418 INFO IntervalArgumentCollection - Processing 2 bp from intervals
16:45:15.418 INFO ValidateBasicSomaticShortMutations - Done initializing engine
16:45:15.421 INFO ProgressMeter - Starting traversal
16:45:15.421 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:45:15.458 INFO ProgressMeter - unmapped 0.0 2 3243.2
16:45:15.458 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
16:45:15.459 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 4:45:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
16:45:15.527 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:45:15.527 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
16:45:15.527 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
16:45:15.527 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
16:45:15.528 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
16:45:15.528 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 4:45:15 PM UTC
16:45:15.528 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:45:15.528 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:45:15.528 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:45:15.528 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:45:15.528 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:45:15.528 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:45:15.528 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
16:45:15.528 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
16:45:15.528 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
16:45:15.528 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
16:45:15.528 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
16:45:15.528 INFO ValidateBasicSomaticShortMutations - Initializing engine
16:45:15.532 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
16:45:15.534 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
16:45:15.538 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
16:45:15.539 INFO ValidateBasicSomaticShortMutations - Done initializing engine
16:45:15.539 INFO ProgressMeter - Starting traversal
16:45:15.539 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:45:16.083 INFO ProgressMeter - unmapped 0.0 336 37058.8
16:45:16.083 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
16:45:16.089 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 4:45:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1140850688