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

16:44:43.168 INFO  BlockManagerInfo - Removed broadcast_180_piece0 on localhost:37215 in memory (size: 63.3 KiB, free: 1919.4 MiB)
16:44:43.169 INFO  ExampleReferenceWalker - ------------------------------------------------------------
16:44:43.169 INFO  ExampleReferenceWalker - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:44:43.169 INFO  ExampleReferenceWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
16:44:43.169 INFO  ExampleReferenceWalker - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:44:43.169 INFO  ExampleReferenceWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:44:43.169 INFO  ExampleReferenceWalker - Start Date/Time: May 27, 2025 at 4:44:43 PM GMT
16:44:43.169 INFO  ExampleReferenceWalker - ------------------------------------------------------------
16:44:43.169 INFO  ExampleReferenceWalker - ------------------------------------------------------------
16:44:43.169 INFO  ExampleReferenceWalker - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:44:43.169 INFO  ExampleReferenceWalker - Picard Version: 3.4.0
16:44:43.169 INFO  ExampleReferenceWalker - Built for Spark Version: 3.5.0
16:44:43.169 INFO  ExampleReferenceWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:44:43.169 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:44:43.169 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:44:43.169 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:44:43.169 INFO  ExampleReferenceWalker - Deflater: IntelDeflater
16:44:43.169 INFO  ExampleReferenceWalker - Inflater: IntelInflater
16:44:43.169 INFO  ExampleReferenceWalker - GCS max retries/reopens: 20
16:44:43.169 INFO  BlockManagerInfo - Removed broadcast_186_piece0 on localhost:37215 in memory (size: 261.5 KiB, free: 1919.7 MiB)
16:44:43.169 INFO  ExampleReferenceWalker - Requester pays: disabled
16:44:43.170 INFO  ExampleReferenceWalker - Initializing engine
16:44:43.170 INFO  BlockManagerInfo - Removed broadcast_182_piece0 on localhost:37215 in memory (size: 261.4 KiB, free: 1919.9 MiB)
16:44:43.171 INFO  BlockManagerInfo - Removed broadcast_183_piece0 on localhost:37215 in memory (size: 63.3 KiB, free: 1920.0 MiB)
16:44:43.173 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf
16:44:43.174 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
16:44:43.174 INFO  ExampleReferenceWalker - Done initializing engine
16:44:43.174 INFO  ProgressMeter - Starting traversal
16:44:43.174 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
16:44:43.185 INFO  ProgressMeter -             unmapped              0.0                   400        2181818.2
16:44:43.185 INFO  ProgressMeter - Traversal complete. Processed 400 total bases in 0.0 minutes.
16:44:43.186 INFO  ExampleReferenceWalker - Shutting down engine
[May 27, 2025 at 4:44:43 PM GMT] org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2193620992