Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest
Tests
| Test |
Duration |
Result |
| testCountBasesInReferenceFull |
0.047s |
passed |
| testCountBasesInReferenceWithInterval |
0.014s |
passed |
| testCountBasesInReferenceWithOutputFile |
0.020s |
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
14:11:06.206 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.206 INFO CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:11:06.206 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
14:11:06.206 INFO CountBasesInReference - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:11:06.206 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:11:06.206 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 2:11:06 PM GMT
14:11:06.206 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.206 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.206 INFO CountBasesInReference - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:11:06.206 INFO CountBasesInReference - Picard Version: 3.4.0
14:11:06.206 INFO CountBasesInReference - Built for Spark Version: 3.5.0
14:11:06.206 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:11:06.206 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:11:06.206 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:11:06.206 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:11:06.206 INFO CountBasesInReference - Deflater: IntelDeflater
14:11:06.206 INFO CountBasesInReference - Inflater: IntelInflater
14:11:06.206 INFO CountBasesInReference - GCS max retries/reopens: 20
14:11:06.206 INFO CountBasesInReference - Requester pays: disabled
14:11:06.206 INFO CountBasesInReference - Initializing engine
14:11:06.206 INFO CountBasesInReference - Done initializing engine
14:11:06.206 INFO ProgressMeter - Starting traversal
14:11:06.206 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
14:11:06.239 INFO ProgressMeter - 4:16000 0.0 64000 120000000.0
14:11:06.239 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
14:11:06.239 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 2:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1461714944
14:11:06.252 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.252 INFO CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:11:06.252 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
14:11:06.252 INFO CountBasesInReference - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:11:06.252 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:11:06.252 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 2:11:06 PM GMT
14:11:06.252 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.252 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.252 INFO CountBasesInReference - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:11:06.252 INFO CountBasesInReference - Picard Version: 3.4.0
14:11:06.252 INFO CountBasesInReference - Built for Spark Version: 3.5.0
14:11:06.252 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:11:06.252 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:11:06.252 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:11:06.252 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:11:06.252 INFO CountBasesInReference - Deflater: IntelDeflater
14:11:06.252 INFO CountBasesInReference - Inflater: IntelInflater
14:11:06.252 INFO CountBasesInReference - GCS max retries/reopens: 20
14:11:06.252 INFO CountBasesInReference - Requester pays: disabled
14:11:06.252 INFO CountBasesInReference - Initializing engine
14:11:06.253 INFO IntervalArgumentCollection - Processing 1001 bp from intervals
14:11:06.253 INFO CountBasesInReference - Done initializing engine
14:11:06.253 INFO ProgressMeter - Starting traversal
14:11:06.253 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
14:11:06.253 INFO ProgressMeter - 1:5999 0.0 1001 Infinity
14:11:06.253 INFO ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
14:11:06.253 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 2:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1461714944
14:11:06.266 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.267 INFO CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g5c95f6f-SNAPSHOT
14:11:06.267 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
14:11:06.267 INFO CountBasesInReference - Executing as root@9cd1444b9593 on Linux v6.11.0-1014-azure amd64
14:11:06.267 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:11:06.267 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 2:11:06 PM GMT
14:11:06.267 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.267 INFO CountBasesInReference - ------------------------------------------------------------
14:11:06.267 INFO CountBasesInReference - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:11:06.267 INFO CountBasesInReference - Picard Version: 3.4.0
14:11:06.267 INFO CountBasesInReference - Built for Spark Version: 3.5.0
14:11:06.267 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:11:06.267 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:11:06.267 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:11:06.267 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:11:06.267 INFO CountBasesInReference - Deflater: IntelDeflater
14:11:06.267 INFO CountBasesInReference - Inflater: IntelInflater
14:11:06.267 INFO CountBasesInReference - GCS max retries/reopens: 20
14:11:06.267 INFO CountBasesInReference - Requester pays: disabled
14:11:06.267 INFO CountBasesInReference - Initializing engine
14:11:06.267 INFO CountBasesInReference - Done initializing engine
14:11:06.267 INFO ProgressMeter - Starting traversal
14:11:06.267 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
14:11:06.273 INFO ProgressMeter - 4:16000 0.0 64000 640000000.0
14:11:06.273 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
14:11:06.273 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 2:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1461714944