Class org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalkerIntegrationTest

AAA Seen: 78 Reads 9 Variants 3
AAC Seen: 1 Reads 0 Variants 1
ACC Seen: 1 Reads 0 Variants 1
CCC Seen: 78 Reads 0 Variants 1
CCG Seen: 1 Reads 0 Variants 0
CGG Seen: 1 Reads 0 Variants 0
GGG Seen: 78 Reads 0 Variants 0
GGT Seen: 1 Reads 0 Variants 0
GTT Seen: 1 Reads 0 Variants 0
NAA Seen: 1 Reads 1 Variants 0
NN Seen: 1 Reads 0 Variants 0
NNA Seen: 1 Reads 1 Variants 0
NNN Seen: 78 Reads 1 Variants 0
TT Seen: 1 Reads 0 Variants 0
TTT Seen: 78 Reads 0 Variants 0

15:56:34.374 INFO  ExampleReferenceWalker - ------------------------------------------------------------
15:56:34.375 INFO  ExampleReferenceWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
15:56:34.375 INFO  ExampleReferenceWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
15:56:34.375 INFO  ExampleReferenceWalker - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
15:56:34.375 INFO  ExampleReferenceWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:56:34.375 INFO  ExampleReferenceWalker - Start Date/Time: May 19, 2025 at 3:56:34 PM GMT
15:56:34.375 INFO  ExampleReferenceWalker - ------------------------------------------------------------
15:56:34.375 INFO  ExampleReferenceWalker - ------------------------------------------------------------
15:56:34.375 INFO  ExampleReferenceWalker - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:56:34.375 INFO  ExampleReferenceWalker - Picard Version: 3.4.0
15:56:34.375 INFO  ExampleReferenceWalker - Built for Spark Version: 3.5.0
15:56:34.375 INFO  ExampleReferenceWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:56:34.375 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:56:34.375 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:56:34.375 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:56:34.375 INFO  ExampleReferenceWalker - Deflater: IntelDeflater
15:56:34.375 INFO  ExampleReferenceWalker - Inflater: IntelInflater
15:56:34.375 INFO  ExampleReferenceWalker - GCS max retries/reopens: 20
15:56:34.375 INFO  ExampleReferenceWalker - Requester pays: disabled
15:56:34.375 INFO  ExampleReferenceWalker - Initializing engine
15:56:34.378 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf
15:56:34.379 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
15:56:34.379 INFO  ExampleReferenceWalker - Done initializing engine
15:56:34.379 INFO  ProgressMeter - Starting traversal
15:56:34.379 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
15:56:34.391 INFO  ProgressMeter -             unmapped              0.0                   400        2000000.0
15:56:34.391 INFO  ProgressMeter - Traversal complete. Processed 400 total bases in 0.0 minutes.
15:56:34.391 INFO  ExampleReferenceWalker - Shutting down engine
[May 19, 2025 at 3:56:34 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2013265920