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

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

tests

failures

ignored

0.052s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testCountBasesInReferenceFull	0.037s	passed
testCountBasesInReferenceWithInterval	0.005s	passed
testCountBasesInReferenceWithOutputFile	0.010s	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

20:51:50.385 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.385 INFO  CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
20:51:50.385 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
20:51:50.385 INFO  CountBasesInReference - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:51:50.385 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:51:50.385 INFO  CountBasesInReference - Start Date/Time: June 12, 2025 at 8:51:50 PM UTC
20:51:50.385 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.385 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.385 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:51:50.385 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:51:50.385 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:51:50.385 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:51:50.385 INFO  CountBasesInReference - Deflater: IntelDeflater
20:51:50.385 INFO  CountBasesInReference - Inflater: IntelInflater
20:51:50.385 INFO  CountBasesInReference - GCS max retries/reopens: 20
20:51:50.385 INFO  CountBasesInReference - Requester pays: disabled
20:51:50.385 INFO  CountBasesInReference - Initializing engine
20:51:50.385 INFO  CountBasesInReference - Done initializing engine
20:51:50.385 INFO  ProgressMeter - Starting traversal
20:51:50.386 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
20:51:50.416 INFO  ProgressMeter -              4:16000              0.0                 64000      128000000.0
20:51:50.416 INFO  ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
20:51:50.416 INFO  CountBasesInReference - Shutting down engine
[June 12, 2025 at 8:51:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
20:51:50.421 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.421 INFO  CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
20:51:50.421 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
20:51:50.421 INFO  CountBasesInReference - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:51:50.421 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:51:50.421 INFO  CountBasesInReference - Start Date/Time: June 12, 2025 at 8:51:50 PM UTC
20:51:50.421 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.421 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.421 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:51:50.421 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:51:50.421 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:51:50.421 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:51:50.421 INFO  CountBasesInReference - Deflater: IntelDeflater
20:51:50.421 INFO  CountBasesInReference - Inflater: IntelInflater
20:51:50.421 INFO  CountBasesInReference - GCS max retries/reopens: 20
20:51:50.421 INFO  CountBasesInReference - Requester pays: disabled
20:51:50.421 INFO  CountBasesInReference - Initializing engine
20:51:50.421 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
20:51:50.421 INFO  CountBasesInReference - Done initializing engine
20:51:50.421 INFO  ProgressMeter - Starting traversal
20:51:50.422 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
20:51:50.422 INFO  ProgressMeter -               1:5999              0.0                  1001         Infinity
20:51:50.422 INFO  ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
20:51:50.422 INFO  CountBasesInReference - Shutting down engine
[June 12, 2025 at 8:51:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
20:51:50.425 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.425 INFO  CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
20:51:50.425 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
20:51:50.425 INFO  CountBasesInReference - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:51:50.425 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:51:50.425 INFO  CountBasesInReference - Start Date/Time: June 12, 2025 at 8:51:50 PM UTC
20:51:50.425 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.425 INFO  CountBasesInReference - ------------------------------------------------------------
20:51:50.425 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:51:50.425 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:51:50.425 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:51:50.425 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:51:50.425 INFO  CountBasesInReference - Deflater: IntelDeflater
20:51:50.425 INFO  CountBasesInReference - Inflater: IntelInflater
20:51:50.425 INFO  CountBasesInReference - GCS max retries/reopens: 20
20:51:50.425 INFO  CountBasesInReference - Requester pays: disabled
20:51:50.425 INFO  CountBasesInReference - Initializing engine
20:51:50.426 INFO  CountBasesInReference - Done initializing engine
20:51:50.426 INFO  ProgressMeter - Starting traversal
20:51:50.426 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
20:51:50.431 INFO  ProgressMeter -              4:16000              0.0                 64000      768000000.0
20:51:50.431 INFO  ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
20:51:50.431 INFO  CountBasesInReference - Shutting down engine
[June 12, 2025 at 8:51:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864