Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest
Tests
| Test |
Duration |
Result |
| testCountBasesInReferenceFull |
0.030s |
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
15:50:35.049 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.049 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
15:50:35.049 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
15:50:35.049 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:50:35.049 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:50:35.049 INFO CountBasesInReference - Start Date/Time: May 19, 2025 at 3:50:35 PM UTC
15:50:35.049 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.049 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.049 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:50:35.049 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:50:35.049 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:50:35.049 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:50:35.049 INFO CountBasesInReference - Deflater: IntelDeflater
15:50:35.049 INFO CountBasesInReference - Inflater: IntelInflater
15:50:35.049 INFO CountBasesInReference - GCS max retries/reopens: 20
15:50:35.049 INFO CountBasesInReference - Requester pays: disabled
15:50:35.049 INFO CountBasesInReference - Initializing engine
15:50:35.050 INFO CountBasesInReference - Done initializing engine
15:50:35.050 INFO ProgressMeter - Starting traversal
15:50:35.050 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
15:50:35.074 INFO ProgressMeter - 4:16000 0.0 64000 160000000.0
15:50:35.075 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
15:50:35.075 INFO CountBasesInReference - Shutting down engine
[May 19, 2025 at 3:50:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
15:50:35.079 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.079 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
15:50:35.079 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
15:50:35.079 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:50:35.079 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:50:35.079 INFO CountBasesInReference - Start Date/Time: May 19, 2025 at 3:50:35 PM UTC
15:50:35.079 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.079 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.079 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:50:35.079 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:50:35.079 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:50:35.079 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:50:35.079 INFO CountBasesInReference - Deflater: IntelDeflater
15:50:35.079 INFO CountBasesInReference - Inflater: IntelInflater
15:50:35.079 INFO CountBasesInReference - GCS max retries/reopens: 20
15:50:35.079 INFO CountBasesInReference - Requester pays: disabled
15:50:35.079 INFO CountBasesInReference - Initializing engine
15:50:35.080 INFO IntervalArgumentCollection - Processing 1001 bp from intervals
15:50:35.080 INFO CountBasesInReference - Done initializing engine
15:50:35.080 INFO ProgressMeter - Starting traversal
15:50:35.080 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
15:50:35.080 INFO ProgressMeter - 1:5999 0.0 1001 Infinity
15:50:35.080 INFO ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
15:50:35.080 INFO CountBasesInReference - Shutting down engine
[May 19, 2025 at 3:50:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
15:50:35.084 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.084 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
15:50:35.084 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
15:50:35.084 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:50:35.084 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:50:35.084 INFO CountBasesInReference - Start Date/Time: May 19, 2025 at 3:50:35 PM UTC
15:50:35.084 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.084 INFO CountBasesInReference - ------------------------------------------------------------
15:50:35.084 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:50:35.084 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:50:35.084 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:50:35.084 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:50:35.084 INFO CountBasesInReference - Deflater: IntelDeflater
15:50:35.084 INFO CountBasesInReference - Inflater: IntelInflater
15:50:35.084 INFO CountBasesInReference - GCS max retries/reopens: 20
15:50:35.084 INFO CountBasesInReference - Requester pays: disabled
15:50:35.084 INFO CountBasesInReference - Initializing engine
15:50:35.084 INFO CountBasesInReference - Done initializing engine
15:50:35.084 INFO ProgressMeter - Starting traversal
15:50:35.084 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
15:50:35.090 INFO ProgressMeter - 4:16000 0.0 64000 640000000.0
15:50:35.090 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
15:50:35.090 INFO CountBasesInReference - Shutting down engine
[May 19, 2025 at 3:50:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864