Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.fasta > CountBasesInReferenceIntegrationTest

tests

failures

ignored

0.054s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testCountBasesInReferenceFull	0.037s	passed
testCountBasesInReferenceWithInterval	0.005s	passed
testCountBasesInReferenceWithOutputFile	0.012s	passed

Standard output

A : 4546
C : 4995
G : 4559
N : 46000
T : 3900
N : 1001
A : 4546
C : 4995
G : 4559
N : 46000
T : 3900

Standard error

14:27:41.297 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.297 INFO  CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
14:27:41.297 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
14:27:41.297 INFO  CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:27:41.297 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:27:41.297 INFO  CountBasesInReference - Start Date/Time: June 2, 2025 at 2:27:41 PM UTC
14:27:41.297 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.297 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.297 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:27:41.297 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:27:41.297 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:27:41.297 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:27:41.297 INFO  CountBasesInReference - Deflater: IntelDeflater
14:27:41.297 INFO  CountBasesInReference - Inflater: IntelInflater
14:27:41.297 INFO  CountBasesInReference - GCS max retries/reopens: 20
14:27:41.297 INFO  CountBasesInReference - Requester pays: disabled
14:27:41.297 INFO  CountBasesInReference - Initializing engine
14:27:41.297 INFO  CountBasesInReference - Done initializing engine
14:27:41.297 INFO  ProgressMeter - Starting traversal
14:27:41.298 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
14:27:41.329 INFO  ProgressMeter -              4:16000              0.0                 64000      123870967.7
14:27:41.329 INFO  ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
14:27:41.329 INFO  CountBasesInReference - Shutting down engine
[June 2, 2025 at 2:27:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
14:27:41.334 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.334 INFO  CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
14:27:41.334 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
14:27:41.334 INFO  CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:27:41.334 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:27:41.334 INFO  CountBasesInReference - Start Date/Time: June 2, 2025 at 2:27:41 PM UTC
14:27:41.334 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.334 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.334 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:27:41.334 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:27:41.334 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:27:41.334 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:27:41.334 INFO  CountBasesInReference - Deflater: IntelDeflater
14:27:41.334 INFO  CountBasesInReference - Inflater: IntelInflater
14:27:41.334 INFO  CountBasesInReference - GCS max retries/reopens: 20
14:27:41.334 INFO  CountBasesInReference - Requester pays: disabled
14:27:41.334 INFO  CountBasesInReference - Initializing engine
14:27:41.335 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
14:27:41.335 INFO  CountBasesInReference - Done initializing engine
14:27:41.335 INFO  ProgressMeter - Starting traversal
14:27:41.335 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
14:27:41.335 INFO  ProgressMeter -               1:5999              0.0                  1001         Infinity
14:27:41.335 INFO  ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
14:27:41.335 INFO  CountBasesInReference - Shutting down engine
[June 2, 2025 at 2:27:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
14:27:41.339 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.339 INFO  CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
14:27:41.339 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
14:27:41.339 INFO  CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:27:41.339 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:27:41.340 INFO  CountBasesInReference - Start Date/Time: June 2, 2025 at 2:27:41 PM UTC
14:27:41.340 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.340 INFO  CountBasesInReference - ------------------------------------------------------------
14:27:41.340 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:27:41.340 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:27:41.340 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:27:41.340 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:27:41.340 INFO  CountBasesInReference - Deflater: IntelDeflater
14:27:41.340 INFO  CountBasesInReference - Inflater: IntelInflater
14:27:41.340 INFO  CountBasesInReference - GCS max retries/reopens: 20
14:27:41.340 INFO  CountBasesInReference - Requester pays: disabled
14:27:41.340 INFO  CountBasesInReference - Initializing engine
14:27:41.340 INFO  CountBasesInReference - Done initializing engine
14:27:41.340 INFO  ProgressMeter - Starting traversal
14:27:41.340 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
14:27:41.347 INFO  ProgressMeter -              4:16000              0.0                 64000      548571428.6
14:27:41.347 INFO  ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
14:27:41.347 INFO  CountBasesInReference - Shutting down engine
[June 2, 2025 at 2:27:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536