Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.124s |
passed |
| testIndelCase |
0.631s |
passed |
Standard error
14:31:59.737 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:31:59.737 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
14:31:59.737 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:59.737 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:31:59.737 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:31:59.737 INFO ValidateBasicSomaticShortMutations - Start Date/Time: June 2, 2025 at 2:31:59 PM UTC
14:31:59.737 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:31:59.737 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:31:59.737 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:59.737 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:59.737 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:59.738 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:59.738 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
14:31:59.738 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
14:31:59.738 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
14:31:59.738 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
14:31:59.738 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:31:59.738 INFO ValidateBasicSomaticShortMutations - Initializing engine
14:31:59.744 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
14:31:59.747 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
14:31:59.747 INFO IntervalArgumentCollection - Processing 2 bp from intervals
14:31:59.748 INFO ValidateBasicSomaticShortMutations - Done initializing engine
14:31:59.751 INFO ProgressMeter - Starting traversal
14:31:59.751 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
14:31:59.790 INFO ProgressMeter - unmapped 0.0 2 3076.9
14:31:59.790 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:31:59.791 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[June 2, 2025 at 2:31:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
14:31:59.865 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:31:59.865 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
14:31:59.865 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:59.865 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:31:59.865 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:31:59.865 INFO ValidateBasicSomaticShortMutations - Start Date/Time: June 2, 2025 at 2:31:59 PM UTC
14:31:59.865 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:31:59.865 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:31:59.865 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:59.865 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:59.865 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:59.865 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:59.865 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
14:31:59.865 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
14:31:59.865 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
14:31:59.865 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
14:31:59.865 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
14:31:59.865 INFO ValidateBasicSomaticShortMutations - Initializing engine
14:31:59.869 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
14:31:59.872 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
14:31:59.875 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
14:31:59.876 INFO ValidateBasicSomaticShortMutations - Done initializing engine
14:31:59.876 INFO ProgressMeter - Starting traversal
14:31:59.876 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
14:32:00.401 INFO ProgressMeter - unmapped 0.0 336 38400.0
14:32:00.401 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
14:32:00.407 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[June 2, 2025 at 2:32:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1302331392