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

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

tests
0

failures
0

ignored
0.983s

duration
100%

successful

Tests

Test Duration Result
testBasic 0.165s passed
testIndelCase 0.818s passed

Standard error

14:15:02.404 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:15:02.404 INFO  ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:15:02.404 INFO  ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
14:15:02.404 INFO  ValidateBasicSomaticShortMutations - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:15:02.404 INFO  ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:15:02.404 INFO  ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 2:15:02 PM GMT
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - Inflater: IntelInflater
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
14:15:02.405 INFO  ValidateBasicSomaticShortMutations - Requester pays: disabled
14:15:02.405 WARN  ValidateBasicSomaticShortMutations - 

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

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

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


14:15:02.405 INFO  ValidateBasicSomaticShortMutations - Initializing engine
14:15:02.413 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
14:15:02.416 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
14:15:02.417 INFO  IntervalArgumentCollection - Processing 2 bp from intervals
14:15:02.417 INFO  ValidateBasicSomaticShortMutations - Done initializing engine
14:15:02.424 INFO  ProgressMeter - Starting traversal
14:15:02.424 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:15:02.474 INFO  ProgressMeter -             unmapped              0.0                     2           2400.0
14:15:02.474 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
14:15:02.476 INFO  ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 2:15:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Start Date/Time: May 27, 2025 at 2:15:02 PM GMT
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Picard Version: 3.4.0
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Built for Spark Version: 3.5.0
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Inflater: IntelInflater
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Requester pays: disabled
14:15:02.611 WARN  ValidateBasicSomaticShortMutations - 

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

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

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


14:15:02.611 INFO  ValidateBasicSomaticShortMutations - Initializing engine
14:15:02.616 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
14:15:02.619 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
14:15:02.623 INFO  IntervalArgumentCollection - Processing 1350 bp from intervals
14:15:02.624 INFO  ValidateBasicSomaticShortMutations - Done initializing engine
14:15:02.624 INFO  ProgressMeter - Starting traversal
14:15:02.624 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:15:03.271 INFO  ProgressMeter -             unmapped              0.0                   336          31159.2
14:15:03.271 INFO  ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
14:15:03.277 INFO  ValidateBasicSomaticShortMutations - Shutting down engine
[May 27, 2025 at 2:15:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000