Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest
Tests
| Test |
Duration |
Result |
| testBasic |
0.126s |
passed |
| testIndelCase |
0.686s |
passed |
Standard error
15:54:43.776 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:54:43.776 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
15:54:43.776 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
15:54:43.776 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:54:43.776 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:54:43.776 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 19, 2025 at 3:54:43 PM UTC
15:54:43.776 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:54:43.776 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:54:43.776 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:54:43.776 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:54:43.776 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:54:43.776 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:54:43.776 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
15:54:43.776 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
15:54:43.776 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
15:54:43.776 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
15:54:43.776 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:54:43.776 INFO ValidateBasicSomaticShortMutations - Initializing engine
15:54:43.783 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
15:54:43.786 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
15:54:43.786 INFO IntervalArgumentCollection - Processing 2 bp from intervals
15:54:43.787 INFO ValidateBasicSomaticShortMutations - Done initializing engine
15:54:43.791 INFO ProgressMeter - Starting traversal
15:54:43.791 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:54:43.830 INFO ProgressMeter - unmapped 0.0 2 3076.9
15:54:43.830 INFO ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
15:54:43.831 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 19, 2025 at 3:54:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
15:54:43.901 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:54:43.901 INFO ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
15:54:43.901 INFO ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
15:54:43.901 INFO ValidateBasicSomaticShortMutations - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:54:43.901 INFO ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:54:43.901 INFO ValidateBasicSomaticShortMutations - Start Date/Time: May 19, 2025 at 3:54:43 PM UTC
15:54:43.901 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:54:43.901 INFO ValidateBasicSomaticShortMutations - ------------------------------------------------------------
15:54:43.901 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:54:43.901 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:54:43.901 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:54:43.902 INFO ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:54:43.902 INFO ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
15:54:43.902 INFO ValidateBasicSomaticShortMutations - Inflater: IntelInflater
15:54:43.902 INFO ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
15:54:43.902 INFO ValidateBasicSomaticShortMutations - Requester pays: disabled
15:54:43.902 WARN ValidateBasicSomaticShortMutations -
?[1m?[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m
15:54:43.902 INFO ValidateBasicSomaticShortMutations - Initializing engine
15:54:43.905 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
15:54:43.908 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
15:54:43.911 INFO IntervalArgumentCollection - Processing 1350 bp from intervals
15:54:43.911 INFO ValidateBasicSomaticShortMutations - Done initializing engine
15:54:43.911 INFO ProgressMeter - Starting traversal
15:54:43.912 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:54:44.498 INFO ProgressMeter - unmapped 0.0 336 34402.7
15:54:44.498 INFO ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
15:54:44.504 INFO ValidateBasicSomaticShortMutations - Shutting down engine
[May 19, 2025 at 3:54:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848