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

all > org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup > ValidateBasicSomaticShortMutationsIntegrationTest
tests
failures
ignored
0.887s
duration
100%
successful
Tests
Standard error
Tests

Test	Duration	Result
testBasic	0.157s	passed
testIndelCase	0.730s	passed
Standard error

22:54:32.010 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
22:54:32.010 INFO  ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
22:54:32.010 INFO  ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
22:54:32.010 INFO  ValidateBasicSomaticShortMutations - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:54:32.010 INFO  ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - Start Date/Time: March 28, 2025 at 10:54:32 PM UTC
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - Inflater: IntelInflater
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
22:54:32.011 INFO  ValidateBasicSomaticShortMutations - Requester pays: disabled
22:54:32.011 WARN  ValidateBasicSomaticShortMutations - 

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

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

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


22:54:32.011 INFO  ValidateBasicSomaticShortMutations - Initializing engine
22:54:32.017 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
22:54:32.021 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
22:54:32.022 INFO  IntervalArgumentCollection - Processing 2 bp from intervals
22:54:32.022 INFO  ValidateBasicSomaticShortMutations - Done initializing engine
22:54:32.033 INFO  ProgressMeter - Starting traversal
22:54:32.033 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:54:32.097 INFO  ProgressMeter -             unmapped              0.0                     2           1875.0
22:54:32.097 INFO  ProgressMeter - Traversal complete. Processed 2 total variants in 0.0 minutes.
22:54:32.099 INFO  ValidateBasicSomaticShortMutations - Shutting down engine
[March 28, 2025 at 10:54:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup vUnavailable
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - For support and documentation go to https://software.broadinstitute.org/gatk/
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - Start Date/Time: March 28, 2025 at 10:54:32 PM UTC
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - ------------------------------------------------------------
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - Deflater: IntelDeflater
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - Inflater: IntelInflater
22:54:32.195 INFO  ValidateBasicSomaticShortMutations - GCS max retries/reopens: 20
22:54:32.196 INFO  ValidateBasicSomaticShortMutations - Requester pays: disabled
22:54:32.196 WARN  ValidateBasicSomaticShortMutations - 

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

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

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


22:54:32.196 INFO  ValidateBasicSomaticShortMutations - Initializing engine
22:54:32.200 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
22:54:32.203 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
22:54:32.206 INFO  IntervalArgumentCollection - Processing 1350 bp from intervals
22:54:32.206 INFO  ValidateBasicSomaticShortMutations - Done initializing engine
22:54:32.206 INFO  ProgressMeter - Starting traversal
22:54:32.207 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:54:32.808 INFO  ProgressMeter -             unmapped              0.0                   336          33544.1
22:54:32.808 INFO  ProgressMeter - Traversal complete. Processed 336 total variants in 0.0 minutes.
22:54:32.813 INFO  ValidateBasicSomaticShortMutations - Shutting down engine
[March 28, 2025 at 10:54:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1178599424