Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.138s |
passed |
| testIndelCase |
0.665s |
passed |
Standard error
20:55:58.742 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
20:55:58.742 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
20:55:58.742 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
20:55:58.742 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:55:58.742 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:55:58.742 INFO ValidateBasicSomaticShortMutations - Start Date/Time: June 12, 2025 at 8:55:58 PM UTC
20:55:58.742 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
20:55:58.742 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
20:55:58.743 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:55:58.743 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:55:58.743 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:55:58.743 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:55:58.743 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
20:55:58.743 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
20:55:58.743 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
20:55:58.743 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
20:55:58.743 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
20:55:58.743 INFO ValidateBasicSomaticShortMutations - Initializing engine
20:55:58.750 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
20:55:58.752 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
20:55:58.753 INFO IntervalArgumentCollection - Processing 2 bp from intervals
20:55:58.753 INFO ValidateBasicSomaticShortMutations - Done initializing engine
20:55:58.757 INFO ProgressMeter - Starting traversal
20:55:58.757 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:55:58.807 INFO ProgressMeter - unmapped 0.0 2 2400.0
20:55:58.807 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
20:55:58.808 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[June 12, 2025 at 8:55:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
20:55:58.878 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
20:55:58.878 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
20:55:58.878 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
20:55:58.878 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:55:58.878 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:55:58.878 INFO ValidateBasicSomaticShortMutations - Start Date/Time: June 12, 2025 at 8:55:58 PM UTC
20:55:58.878 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
20:55:58.878 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
20:55:58.879 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:55:58.879 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:55:58.879 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:55:58.879 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:55:58.879 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
20:55:58.879 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
20:55:58.879 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
20:55:58.879 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
20:55:58.879 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
20:55:58.879 INFO ValidateBasicSomaticShortMutations - Initializing engine
20:55:58.882 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
20:55:58.884 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
20:55:58.889 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
20:55:58.889 INFO ValidateBasicSomaticShortMutations - Done initializing engine
20:55:58.889 INFO ProgressMeter - Starting traversal
20:55:58.889 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
20:55:59.455 INFO ProgressMeter - unmapped 0.0 336 35618.4
20:55:59.455 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
20:55:59.460 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[June 12, 2025 at 8:55:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1616904192