Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.160s |
passed |
| testIndelCase |
0.787s |
passed |
Standard error
15:07:28.146 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:07:28.146 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
15:07:28.146 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:28.147 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:07:28.147 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:07:28.147 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 3:07:28 PM UTC
15:07:28.147 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:07:28.147 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:07:28.147 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:28.147 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:28.147 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:28.147 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:28.147 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
15:07:28.147 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
15:07:28.147 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
15:07:28.147 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
15:07:28.147 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:07:28.147 INFO ValidateBasicSomaticShortMutations - Initializing engine
15:07:28.153 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
15:07:28.157 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
15:07:28.158 INFO IntervalArgumentCollection - Processing 2 bp from intervals
15:07:28.158 INFO ValidateBasicSomaticShortMutations - Done initializing engine
15:07:28.164 INFO ProgressMeter - Starting traversal
15:07:28.164 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:07:28.215 INFO ProgressMeter - unmapped 0.0 2 2352.9
15:07:28.215 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:07:28.217 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 3:07:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
15:07:28.309 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:07:28.310 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
15:07:28.310 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
15:07:28.310 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:07:28.310 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:07:28.310 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 3:07:28 PM UTC
15:07:28.310 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:07:28.310 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:07:28.310 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:07:28.310 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:07:28.310 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:07:28.310 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:07:28.310 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
15:07:28.310 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
15:07:28.310 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
15:07:28.310 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
15:07:28.310 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:07:28.310 INFO ValidateBasicSomaticShortMutations - Initializing engine
15:07:28.314 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
15:07:28.317 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
15:07:28.321 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
15:07:28.321 INFO ValidateBasicSomaticShortMutations - Done initializing engine
15:07:28.321 INFO ProgressMeter - Starting traversal
15:07:28.321 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:07:28.983 INFO ProgressMeter - unmapped 0.0 336 30453.2
15:07:28.983 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
15:07:28.989 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 3:07:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1839202304