Class org.broadinstitute.hellbender.engine.MultiplePassVariantWalkerUnitTest
Tests
Test |
Duration |
Result |
testTwoPassTraversal |
0.011s |
passed |
Standard error
18:46:04.767 INFO DummyMultiplePassVariantWalker - ------------------------------------------------------------
18:46:04.768 INFO DummyMultiplePassVariantWalker - org.broadinstitute.hellbender.engine vUnavailable
18:46:04.768 INFO DummyMultiplePassVariantWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
18:46:04.768 INFO DummyMultiplePassVariantWalker - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:46:04.768 INFO DummyMultiplePassVariantWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:46:04.768 INFO DummyMultiplePassVariantWalker - Start Date/Time: May 19, 2025 at 6:46:04 PM UTC
18:46:04.768 INFO DummyMultiplePassVariantWalker - ------------------------------------------------------------
18:46:04.768 INFO DummyMultiplePassVariantWalker - ------------------------------------------------------------
18:46:04.768 INFO DummyMultiplePassVariantWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:46:04.768 INFO DummyMultiplePassVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:46:04.768 INFO DummyMultiplePassVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:46:04.768 INFO DummyMultiplePassVariantWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:46:04.768 INFO DummyMultiplePassVariantWalker - Deflater: IntelDeflater
18:46:04.768 INFO DummyMultiplePassVariantWalker - Inflater: IntelInflater
18:46:04.768 INFO DummyMultiplePassVariantWalker - GCS max retries/reopens: 20
18:46:04.768 INFO DummyMultiplePassVariantWalker - Requester pays: disabled
18:46:04.768 INFO DummyMultiplePassVariantWalker - Initializing engine
18:46:04.769 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/multiallelic.vcf
18:46:04.770 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/multiallelic.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:46:04.771 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/multiallelic.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:46:04.771 WARN IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/multiallelic.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
18:46:04.771 INFO DummyMultiplePassVariantWalker - Done initializing engine
18:46:04.771 INFO ProgressMeter - Starting traversal
18:46:04.771 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:46:04.771 INFO DummyMultiplePassVariantWalker - Starting pass 0 through the variants
18:46:04.773 INFO DummyMultiplePassVariantWalker - Finished pass 0 through the variants
18:46:04.773 INFO DummyMultiplePassVariantWalker - Starting pass 1 through the variants
18:46:04.774 INFO DummyMultiplePassVariantWalker - Finished pass 1 through the variants
18:46:04.774 INFO DummyMultiplePassVariantWalker - No variants filtered by: AllowAllVariantsVariantFilter
18:46:04.774 INFO DummyMultiplePassVariantWalker - 0 read(s) filtered by: AllowAllReadsReadFilter
18:46:04.774 INFO ProgressMeter - unmapped 0.0 104 2080000.0
18:46:04.774 INFO ProgressMeter - Traversal complete. Processed 104 total variants in 0.0 minutes.
18:46:04.774 INFO DummyMultiplePassVariantWalker - Shutting down engine
[May 19, 2025 at 6:46:04 PM UTC] org.broadinstitute.hellbender.engine.MultiplePassVariantWalkerUnitTest$DummyMultiplePassVariantWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600