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

13:59:42.505 INFO  ExampleReferenceWalker - ------------------------------------------------------------
13:59:42.505 INFO  ExampleReferenceWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
13:59:42.505 INFO  ExampleReferenceWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
13:59:42.505 INFO  ExampleReferenceWalker - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
13:59:42.505 INFO  ExampleReferenceWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
13:59:42.506 INFO  ExampleReferenceWalker - Start Date/Time: May 27, 2025 at 1:59:42 PM GMT
13:59:42.506 INFO  ExampleReferenceWalker - ------------------------------------------------------------
13:59:42.506 INFO  ExampleReferenceWalker - ------------------------------------------------------------
13:59:42.506 INFO  ExampleReferenceWalker - HTSJDK Version: test_cram_wiring-SNAPSHOT
13:59:42.506 INFO  ExampleReferenceWalker - Picard Version: 3.4.0
13:59:42.506 INFO  ExampleReferenceWalker - Built for Spark Version: 3.5.0
13:59:42.506 INFO  ExampleReferenceWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:59:42.506 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:59:42.506 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:59:42.506 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:59:42.506 INFO  ExampleReferenceWalker - Deflater: IntelDeflater
13:59:42.506 INFO  ExampleReferenceWalker - Inflater: IntelInflater
13:59:42.506 INFO  ExampleReferenceWalker - GCS max retries/reopens: 20
13:59:42.506 INFO  ExampleReferenceWalker - Requester pays: disabled
13:59:42.506 INFO  ExampleReferenceWalker - Initializing engine
13:59:42.508 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf
13:59:42.508 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
13:59:42.508 INFO  ExampleReferenceWalker - Done initializing engine
13:59:42.508 INFO  ProgressMeter - Starting traversal
13:59:42.509 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
13:59:42.515 INFO  ProgressMeter -             unmapped              0.0                   400        4000000.0
13:59:42.515 INFO  ProgressMeter - Traversal complete. Processed 400 total bases in 0.0 minutes.
13:59:42.516 INFO  ExampleReferenceWalker - Shutting down engine
[May 27, 2025 at 1:59:42 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2602565632