Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest
Tests
| Test |
Duration |
Result |
| testCountBasesInReferenceFull |
0.033s |
passed |
| testCountBasesInReferenceWithInterval |
0.004s |
passed |
| testCountBasesInReferenceWithOutputFile |
0.009s |
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
22:50:33.321 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.321 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
22:50:33.321 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
22:50:33.321 INFO CountBasesInReference - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:50:33.321 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:50:33.321 INFO CountBasesInReference - Start Date/Time: March 28, 2025 at 10:50:33 PM UTC
22:50:33.321 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.321 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.321 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:50:33.321 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:50:33.321 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:50:33.321 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:50:33.321 INFO CountBasesInReference - Deflater: IntelDeflater
22:50:33.321 INFO CountBasesInReference - Inflater: IntelInflater
22:50:33.321 INFO CountBasesInReference - GCS max retries/reopens: 20
22:50:33.321 INFO CountBasesInReference - Requester pays: disabled
22:50:33.321 INFO CountBasesInReference - Initializing engine
22:50:33.321 INFO CountBasesInReference - Done initializing engine
22:50:33.321 INFO ProgressMeter - Starting traversal
22:50:33.321 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
22:50:33.350 INFO ProgressMeter - 4:16000 0.0 64000 132413793.1
22:50:33.350 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
22:50:33.350 INFO CountBasesInReference - Shutting down engine
[March 28, 2025 at 10:50:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1447034880
22:50:33.354 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.354 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
22:50:33.354 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
22:50:33.354 INFO CountBasesInReference - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:50:33.354 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:50:33.354 INFO CountBasesInReference - Start Date/Time: March 28, 2025 at 10:50:33 PM UTC
22:50:33.354 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.354 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.354 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:50:33.354 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:50:33.354 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:50:33.354 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:50:33.354 INFO CountBasesInReference - Deflater: IntelDeflater
22:50:33.354 INFO CountBasesInReference - Inflater: IntelInflater
22:50:33.354 INFO CountBasesInReference - GCS max retries/reopens: 20
22:50:33.355 INFO CountBasesInReference - Requester pays: disabled
22:50:33.355 INFO CountBasesInReference - Initializing engine
22:50:33.355 INFO IntervalArgumentCollection - Processing 1001 bp from intervals
22:50:33.355 INFO CountBasesInReference - Done initializing engine
22:50:33.355 INFO ProgressMeter - Starting traversal
22:50:33.355 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
22:50:33.355 INFO ProgressMeter - 1:5999 0.0 1001 Infinity
22:50:33.355 INFO ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
22:50:33.355 INFO CountBasesInReference - Shutting down engine
[March 28, 2025 at 10:50:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1447034880
22:50:33.358 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.358 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
22:50:33.358 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
22:50:33.358 INFO CountBasesInReference - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:50:33.358 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:50:33.358 INFO CountBasesInReference - Start Date/Time: March 28, 2025 at 10:50:33 PM UTC
22:50:33.358 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.358 INFO CountBasesInReference - ------------------------------------------------------------
22:50:33.358 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:50:33.358 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:50:33.358 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:50:33.358 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:50:33.358 INFO CountBasesInReference - Deflater: IntelDeflater
22:50:33.358 INFO CountBasesInReference - Inflater: IntelInflater
22:50:33.358 INFO CountBasesInReference - GCS max retries/reopens: 20
22:50:33.358 INFO CountBasesInReference - Requester pays: disabled
22:50:33.358 INFO CountBasesInReference - Initializing engine
22:50:33.359 INFO CountBasesInReference - Done initializing engine
22:50:33.359 INFO ProgressMeter - Starting traversal
22:50:33.359 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
22:50:33.364 INFO ProgressMeter - 4:16000 0.0 64000 768000000.0
22:50:33.364 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
22:50:33.364 INFO CountBasesInReference - Shutting down engine
[March 28, 2025 at 10:50:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1447034880