Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest
Tests
| Test |
Duration |
Result |
| testCountBasesInReferenceFull |
0.040s |
passed |
| testCountBasesInReferenceWithInterval |
0.015s |
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
21:06:44.929 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.929 INFO CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:06:44.929 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
21:06:44.929 INFO CountBasesInReference - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:06:44.929 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:06:44.929 INFO CountBasesInReference - Start Date/Time: June 12, 2025 at 9:06:44 PM GMT
21:06:44.929 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.929 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.929 INFO CountBasesInReference - HTSJDK Version: 4.2.0
21:06:44.929 INFO CountBasesInReference - Picard Version: 3.4.0
21:06:44.929 INFO CountBasesInReference - Built for Spark Version: 3.5.0
21:06:44.929 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:06:44.929 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:06:44.929 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:06:44.929 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:06:44.929 INFO CountBasesInReference - Deflater: IntelDeflater
21:06:44.929 INFO CountBasesInReference - Inflater: IntelInflater
21:06:44.929 INFO CountBasesInReference - GCS max retries/reopens: 20
21:06:44.929 INFO CountBasesInReference - Requester pays: disabled
21:06:44.929 INFO CountBasesInReference - Initializing engine
21:06:44.929 INFO CountBasesInReference - Done initializing engine
21:06:44.929 INFO ProgressMeter - Starting traversal
21:06:44.929 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
21:06:44.955 INFO ProgressMeter - 4:16000 0.0 64000 147692307.7
21:06:44.955 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
21:06:44.955 INFO CountBasesInReference - Shutting down engine
[June 12, 2025 at 9:06:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1920991232
21:06:44.968 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.968 INFO CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:06:44.968 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
21:06:44.968 INFO CountBasesInReference - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:06:44.968 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:06:44.968 INFO CountBasesInReference - Start Date/Time: June 12, 2025 at 9:06:44 PM GMT
21:06:44.968 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.968 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.969 INFO CountBasesInReference - HTSJDK Version: 4.2.0
21:06:44.969 INFO CountBasesInReference - Picard Version: 3.4.0
21:06:44.969 INFO CountBasesInReference - Built for Spark Version: 3.5.0
21:06:44.969 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:06:44.969 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:06:44.969 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:06:44.969 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:06:44.969 INFO CountBasesInReference - Deflater: IntelDeflater
21:06:44.969 INFO CountBasesInReference - Inflater: IntelInflater
21:06:44.969 INFO CountBasesInReference - GCS max retries/reopens: 20
21:06:44.969 INFO CountBasesInReference - Requester pays: disabled
21:06:44.969 INFO CountBasesInReference - Initializing engine
21:06:44.969 INFO IntervalArgumentCollection - Processing 1001 bp from intervals
21:06:44.969 INFO CountBasesInReference - Done initializing engine
21:06:44.969 INFO ProgressMeter - Starting traversal
21:06:44.969 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
21:06:44.969 INFO ProgressMeter - 1:5999 0.0 1001 Infinity
21:06:44.969 INFO ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
21:06:44.970 INFO CountBasesInReference - Shutting down engine
[June 12, 2025 at 9:06:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1920991232
21:06:44.983 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.983 INFO CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:06:44.983 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
21:06:44.983 INFO CountBasesInReference - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:06:44.983 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:06:44.983 INFO CountBasesInReference - Start Date/Time: June 12, 2025 at 9:06:44 PM GMT
21:06:44.983 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.983 INFO CountBasesInReference - ------------------------------------------------------------
21:06:44.984 INFO CountBasesInReference - HTSJDK Version: 4.2.0
21:06:44.984 INFO CountBasesInReference - Picard Version: 3.4.0
21:06:44.984 INFO CountBasesInReference - Built for Spark Version: 3.5.0
21:06:44.984 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:06:44.984 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:06:44.984 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:06:44.984 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:06:44.984 INFO CountBasesInReference - Deflater: IntelDeflater
21:06:44.984 INFO CountBasesInReference - Inflater: IntelInflater
21:06:44.984 INFO CountBasesInReference - GCS max retries/reopens: 20
21:06:44.984 INFO CountBasesInReference - Requester pays: disabled
21:06:44.984 INFO CountBasesInReference - Initializing engine
21:06:44.984 INFO CountBasesInReference - Done initializing engine
21:06:44.984 INFO ProgressMeter - Starting traversal
21:06:44.984 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
21:06:44.990 INFO ProgressMeter - 4:16000 0.0 64000 640000000.0
21:06:44.990 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
21:06:44.990 INFO CountBasesInReference - Shutting down engine
[June 12, 2025 at 9:06:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1920991232