Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest
Tests
| Test |
Duration |
Result |
| testCountBasesInReferenceFull |
0.036s |
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
18:21:01.407 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.407 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
18:21:01.407 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
18:21:01.407 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:21:01.407 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:21:01.407 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 6:21:01 PM UTC
18:21:01.407 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.407 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.407 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:21:01.407 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:21:01.407 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:21:01.407 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:21:01.407 INFO CountBasesInReference - Deflater: IntelDeflater
18:21:01.407 INFO CountBasesInReference - Inflater: IntelInflater
18:21:01.407 INFO CountBasesInReference - GCS max retries/reopens: 20
18:21:01.407 INFO CountBasesInReference - Requester pays: disabled
18:21:01.407 INFO CountBasesInReference - Initializing engine
18:21:01.407 INFO CountBasesInReference - Done initializing engine
18:21:01.407 INFO ProgressMeter - Starting traversal
18:21:01.407 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
18:21:01.438 INFO ProgressMeter - 4:16000 0.0 64000 123870967.7
18:21:01.438 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
18:21:01.438 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 6:21:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1956642816
18:21:01.443 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.443 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
18:21:01.443 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
18:21:01.443 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:21:01.443 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:21:01.443 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 6:21:01 PM UTC
18:21:01.443 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.443 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.443 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:21:01.443 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:21:01.443 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:21:01.443 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:21:01.443 INFO CountBasesInReference - Deflater: IntelDeflater
18:21:01.443 INFO CountBasesInReference - Inflater: IntelInflater
18:21:01.443 INFO CountBasesInReference - GCS max retries/reopens: 20
18:21:01.443 INFO CountBasesInReference - Requester pays: disabled
18:21:01.443 INFO CountBasesInReference - Initializing engine
18:21:01.443 INFO IntervalArgumentCollection - Processing 1001 bp from intervals
18:21:01.443 INFO CountBasesInReference - Done initializing engine
18:21:01.443 INFO ProgressMeter - Starting traversal
18:21:01.443 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
18:21:01.444 INFO ProgressMeter - 1:5999 0.0 1001 60060000.0
18:21:01.444 INFO ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
18:21:01.444 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 6:21:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1956642816
18:21:01.447 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.447 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
18:21:01.447 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
18:21:01.447 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:21:01.447 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:21:01.447 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 6:21:01 PM UTC
18:21:01.447 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.447 INFO CountBasesInReference - ------------------------------------------------------------
18:21:01.447 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:21:01.447 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:21:01.447 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:21:01.447 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:21:01.447 INFO CountBasesInReference - Deflater: IntelDeflater
18:21:01.447 INFO CountBasesInReference - Inflater: IntelInflater
18:21:01.447 INFO CountBasesInReference - GCS max retries/reopens: 20
18:21:01.447 INFO CountBasesInReference - Requester pays: disabled
18:21:01.447 INFO CountBasesInReference - Initializing engine
18:21:01.448 INFO CountBasesInReference - Done initializing engine
18:21:01.448 INFO ProgressMeter - Starting traversal
18:21:01.448 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
18:21:01.453 INFO ProgressMeter - 4:16000 0.0 64000 768000000.0
18:21:01.453 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
18:21:01.454 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 6:21:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1956642816