Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest
Tests
| Test |
Duration |
Result |
| testCountBasesInReferenceFull |
0.031s |
passed |
| testCountBasesInReferenceWithInterval |
0.007s |
passed |
| testCountBasesInReferenceWithOutputFile |
0.016s |
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
13:55:33.510 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.510 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
13:55:33.510 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
13:55:33.510 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:55:33.510 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:55:33.510 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 1:55:33 PM UTC
13:55:33.510 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.510 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.510 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:55:33.510 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:55:33.510 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:55:33.510 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:55:33.510 INFO CountBasesInReference - Deflater: IntelDeflater
13:55:33.510 INFO CountBasesInReference - Inflater: IntelInflater
13:55:33.510 INFO CountBasesInReference - GCS max retries/reopens: 20
13:55:33.510 INFO CountBasesInReference - Requester pays: disabled
13:55:33.510 INFO CountBasesInReference - Initializing engine
13:55:33.510 INFO CountBasesInReference - Done initializing engine
13:55:33.510 INFO ProgressMeter - Starting traversal
13:55:33.510 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
13:55:33.535 INFO ProgressMeter - 4:16000 0.0 64000 153600000.0
13:55:33.536 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
13:55:33.536 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 1:55:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
13:55:33.542 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.542 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
13:55:33.542 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
13:55:33.542 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:55:33.542 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:55:33.542 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 1:55:33 PM UTC
13:55:33.542 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.542 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.542 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:55:33.542 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:55:33.542 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:55:33.542 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:55:33.542 INFO CountBasesInReference - Deflater: IntelDeflater
13:55:33.542 INFO CountBasesInReference - Inflater: IntelInflater
13:55:33.542 INFO CountBasesInReference - GCS max retries/reopens: 20
13:55:33.542 INFO CountBasesInReference - Requester pays: disabled
13:55:33.542 INFO CountBasesInReference - Initializing engine
13:55:33.543 INFO IntervalArgumentCollection - Processing 1001 bp from intervals
13:55:33.543 INFO CountBasesInReference - Done initializing engine
13:55:33.543 INFO ProgressMeter - Starting traversal
13:55:33.543 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
13:55:33.543 INFO ProgressMeter - 1:5999 0.0 1001 Infinity
13:55:33.543 INFO ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
13:55:33.543 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 1:55:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
13:55:33.548 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.548 INFO CountBasesInReference - org.broadinstitute.hellbender.tools.walkers.fasta vUnavailable
13:55:33.548 INFO CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
13:55:33.548 INFO CountBasesInReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:55:33.548 INFO CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:55:33.548 INFO CountBasesInReference - Start Date/Time: May 27, 2025 at 1:55:33 PM UTC
13:55:33.548 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.548 INFO CountBasesInReference - ------------------------------------------------------------
13:55:33.548 INFO CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:55:33.548 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:55:33.548 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:55:33.548 INFO CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:55:33.548 INFO CountBasesInReference - Deflater: IntelDeflater
13:55:33.548 INFO CountBasesInReference - Inflater: IntelInflater
13:55:33.548 INFO CountBasesInReference - GCS max retries/reopens: 20
13:55:33.548 INFO CountBasesInReference - Requester pays: disabled
13:55:33.548 INFO CountBasesInReference - Initializing engine
13:55:33.548 INFO CountBasesInReference - Done initializing engine
13:55:33.548 INFO ProgressMeter - Starting traversal
13:55:33.548 INFO ProgressMeter - Current Locus Elapsed Minutes Bases Processed Bases/Minute
13:55:33.558 INFO ProgressMeter - 4:16000 0.0 64000 384000000.0
13:55:33.558 INFO ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
13:55:33.558 INFO CountBasesInReference - Shutting down engine
[May 27, 2025 at 1:55:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288