Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.148s |
passed |
| testIndelCase |
0.602s |
passed |
Standard error
13:59:40.481 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
13:59:40.481 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
13:59:40.481 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
13:59:40.481 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:59:40.481 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:59:40.481 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 1:59:40 PM UTC
13:59:40.481 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
13:59:40.481 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
13:59:40.482 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:59:40.482 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:59:40.482 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:59:40.482 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:59:40.482 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
13:59:40.482 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
13:59:40.482 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
13:59:40.482 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
13:59:40.482 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
13:59:40.482 INFO ValidateBasicSomaticShortMutations - Initializing engine
13:59:40.488 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
13:59:40.490 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
13:59:40.491 INFO IntervalArgumentCollection - Processing 2 bp from intervals
13:59:40.491 INFO ValidateBasicSomaticShortMutations - Done initializing engine
13:59:40.495 INFO ProgressMeter - Starting traversal
13:59:40.495 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:59:40.532 INFO ProgressMeter - unmapped 0.0 2 3243.2
13:59:40.533 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
13:59:40.534 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 1:59:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
13:59:40.604 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
13:59:40.604 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
13:59:40.604 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
13:59:40.604 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:59:40.604 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:59:40.604 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 1:59:40 PM UTC
13:59:40.604 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
13:59:40.604 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
13:59:40.604 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:59:40.604 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:59:40.604 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:59:40.604 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:59:40.604 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
13:59:40.604 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
13:59:40.604 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
13:59:40.604 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
13:59:40.604 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
13:59:40.604 INFO ValidateBasicSomaticShortMutations - Initializing engine
13:59:40.609 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
13:59:40.611 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
13:59:40.616 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
13:59:40.616 INFO ValidateBasicSomaticShortMutations - Done initializing engine
13:59:40.616 INFO ProgressMeter - Starting traversal
13:59:40.616 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:59:41.114 INFO ProgressMeter - unmapped 0.0 336 40481.9
13:59:41.114 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
13:59:41.120 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 1:59:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1220542464