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

all > org.broadinstitute.hellbender.tools.examples > ExampleReferenceWalkerIntegrationTest

tests

failures

ignored

0.019s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testExampleReferenceWalker	0.019s	passed

Standard output

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

Standard error

22:40:28.555 INFO  ExampleReferenceWalker - ------------------------------------------------------------
22:40:28.556 INFO  ExampleReferenceWalker - org.broadinstitute.hellbender.tools.examples vUnavailable
22:40:28.556 INFO  ExampleReferenceWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
22:40:28.556 INFO  ExampleReferenceWalker - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:40:28.556 INFO  ExampleReferenceWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:40:28.556 INFO  ExampleReferenceWalker - Start Date/Time: March 28, 2025 at 10:40:28 PM UTC
22:40:28.556 INFO  ExampleReferenceWalker - ------------------------------------------------------------
22:40:28.556 INFO  ExampleReferenceWalker - ------------------------------------------------------------
22:40:28.556 INFO  ExampleReferenceWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:40:28.556 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:40:28.556 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:40:28.556 INFO  ExampleReferenceWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:40:28.556 INFO  ExampleReferenceWalker - Deflater: IntelDeflater
22:40:28.556 INFO  ExampleReferenceWalker - Inflater: IntelInflater
22:40:28.556 INFO  ExampleReferenceWalker - GCS max retries/reopens: 20
22:40:28.556 INFO  ExampleReferenceWalker - Requester pays: disabled
22:40:28.556 INFO  ExampleReferenceWalker - Initializing engine
22:40:28.559 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.vcf
22:40:28.559 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/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
22:40:28.560 INFO  ExampleReferenceWalker - Done initializing engine
22:40:28.560 INFO  ProgressMeter - Starting traversal
22:40:28.560 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
22:40:28.568 INFO  ProgressMeter -             unmapped              0.0                   400        3000000.0
22:40:28.568 INFO  ProgressMeter - Traversal complete. Processed 400 total bases in 0.0 minutes.
22:40:28.569 INFO  ExampleReferenceWalker - Shutting down engine
[March 28, 2025 at 10:40:28 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2210398208