Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.123s |
passed |
| testIndelCase |
0.637s |
passed |
Standard error
18:25:07.773 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:25:07.773 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
18:25:07.773 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
18:25:07.773 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:25:07.773 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:25:07.773 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 6:25:07 PM UTC
18:25:07.773 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:25:07.773 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:25:07.773 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:25:07.774 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:25:07.774 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:25:07.774 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:25:07.774 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
18:25:07.774 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
18:25:07.774 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
18:25:07.774 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
18:25:07.774 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:25:07.774 INFO ValidateBasicSomaticShortMutations - Initializing engine
18:25:07.780 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
18:25:07.782 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
18:25:07.783 INFO IntervalArgumentCollection - Processing 2 bp from intervals
18:25:07.783 INFO ValidateBasicSomaticShortMutations - Done initializing engine
18:25:07.786 INFO ProgressMeter - Starting traversal
18:25:07.786 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:25:07.829 INFO ProgressMeter - unmapped 0.0 2 2790.7
18:25:07.829 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
18:25:07.830 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 6:25:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
18:25:07.898 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:25:07.899 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
18:25:07.899 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
18:25:07.899 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:25:07.899 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:25:07.899 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 6:25:07 PM UTC
18:25:07.899 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:25:07.899 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
18:25:07.899 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:25:07.899 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:25:07.899 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:25:07.899 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:25:07.899 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
18:25:07.899 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
18:25:07.899 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
18:25:07.899 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
18:25:07.899 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
18:25:07.899 INFO ValidateBasicSomaticShortMutations - Initializing engine
18:25:07.902 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
18:25:07.905 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
18:25:07.908 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
18:25:07.909 INFO ValidateBasicSomaticShortMutations - Done initializing engine
18:25:07.909 INFO ProgressMeter - Starting traversal
18:25:07.909 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:25:08.447 INFO ProgressMeter - unmapped 0.0 336 37472.1
18:25:08.447 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
18:25:08.452 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 6:25:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1969225728