Class org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup > ValidateBasicSomaticShortMutationsIntegrationTest
2

tests
0

failures
0

ignored
0.947s

duration
100%

successful

Tests

Test Duration Result
testBasic 0.159s passed
testIndelCase 0.788s passed

Standard error

16:10:32.980 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 4:10:32 PM GMT
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
16:10:32.980 INFO  ValidateBasicSomaticShortMutations - Inflater: IntelInflater
16:10:32.981 INFO  ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
16:10:32.981 INFO  ValidateBasicSomaticShortMutations - Requester pays: disabled
16:10:32.981 WARN  ValidateBasicSomaticShortMutations - 

?[1m?[31m   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m


16:10:32.981 INFO  ValidateBasicSomaticShortMutations - Initializing engine
16:10:32.987 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf
16:10:32.990 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf
16:10:32.991 INFO  IntervalArgumentCollection - Processing 2 bp from intervals
16:10:32.991 INFO  ValidateBasicSomaticShortMutations - Done initializing engine
16:10:32.997 INFO  ProgressMeter - Starting traversal
16:10:32.997 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
16:10:33.046 INFO  ProgressMeter -             unmapped              0.0                     2           2449.0
16:10:33.046 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
16:10:33.048 INFO  ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 4:10:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
16:10:33.176 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:10:33.176 INFO  ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
16:10:33.176 INFO  ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
16:10:33.176 INFO  ValidateBasicSomaticShortMutations - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
16:10:33.176 INFO  ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:10:33.176 INFO  ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 4:10:33 PM GMT
16:10:33.176 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:10:33.176 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - Inflater: IntelInflater
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
16:10:33.177 INFO  ValidateBasicSomaticShortMutations - Requester pays: disabled
16:10:33.177 WARN  ValidateBasicSomaticShortMutations - 

?[1m?[31m   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: ValidateBasicSomaticShortMutations is an EXPERIMENTAL tool and should not be used for production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?[0m


16:10:33.177 INFO  ValidateBasicSomaticShortMutations - Initializing engine
16:10:33.181 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf
16:10:33.185 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/IS3.snv.indel.sv-vs-G15512.prenormal.sorted.vcf
16:10:33.189 INFO  IntervalArgumentCollection - Processing 1350 bp from intervals
16:10:33.189 INFO  ValidateBasicSomaticShortMutations - Done initializing engine
16:10:33.189 INFO  ProgressMeter - Starting traversal
16:10:33.190 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
16:10:33.814 INFO  ProgressMeter -             unmapped              0.0                   336          32307.7
16:10:33.814 INFO  ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
16:10:33.821 INFO  ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 4:10:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1119879168