Class org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.fasta > CountBasesInReferenceIntegrationTest

tests

failures

ignored

0.079s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testCountBasesInReferenceFull	0.043s	passed
testCountBasesInReferenceWithInterval	0.014s	passed
testCountBasesInReferenceWithOutputFile	0.022s	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

19:20:02.893 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.893 INFO  CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:20:02.893 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
19:20:02.893 INFO  CountBasesInReference - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:20:02.893 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:20:02.893 INFO  CountBasesInReference - Start Date/Time: May 19, 2025 at 7:20:02 PM GMT
19:20:02.893 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.893 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.894 INFO  CountBasesInReference - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:20:02.894 INFO  CountBasesInReference - Picard Version: 3.4.0
19:20:02.894 INFO  CountBasesInReference - Built for Spark Version: 3.5.0
19:20:02.894 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:20:02.894 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:20:02.894 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:20:02.894 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:20:02.894 INFO  CountBasesInReference - Deflater: IntelDeflater
19:20:02.894 INFO  CountBasesInReference - Inflater: IntelInflater
19:20:02.894 INFO  CountBasesInReference - GCS max retries/reopens: 20
19:20:02.894 INFO  CountBasesInReference - Requester pays: disabled
19:20:02.894 INFO  CountBasesInReference - Initializing engine
19:20:02.894 INFO  CountBasesInReference - Done initializing engine
19:20:02.894 INFO  ProgressMeter - Starting traversal
19:20:02.894 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
19:20:02.923 INFO  ProgressMeter -              4:16000              0.0                 64000      132413793.1
19:20:02.923 INFO  ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
19:20:02.923 INFO  CountBasesInReference - Shutting down engine
[May 19, 2025 at 7:20:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1738539008
19:20:02.936 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.936 INFO  CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:20:02.936 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
19:20:02.936 INFO  CountBasesInReference - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:20:02.936 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:20:02.936 INFO  CountBasesInReference - Start Date/Time: May 19, 2025 at 7:20:02 PM GMT
19:20:02.936 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.936 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.936 INFO  CountBasesInReference - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:20:02.936 INFO  CountBasesInReference - Picard Version: 3.4.0
19:20:02.936 INFO  CountBasesInReference - Built for Spark Version: 3.5.0
19:20:02.936 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:20:02.936 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:20:02.936 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:20:02.936 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:20:02.937 INFO  CountBasesInReference - Deflater: IntelDeflater
19:20:02.937 INFO  CountBasesInReference - Inflater: IntelInflater
19:20:02.937 INFO  CountBasesInReference - GCS max retries/reopens: 20
19:20:02.937 INFO  CountBasesInReference - Requester pays: disabled
19:20:02.937 INFO  CountBasesInReference - Initializing engine
19:20:02.937 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
19:20:02.937 INFO  CountBasesInReference - Done initializing engine
19:20:02.937 INFO  ProgressMeter - Starting traversal
19:20:02.937 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
19:20:02.937 INFO  ProgressMeter -               1:5999              0.0                  1001         Infinity
19:20:02.937 INFO  ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
19:20:02.937 INFO  CountBasesInReference - Shutting down engine
[May 19, 2025 at 7:20:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1738539008
19:20:02.953 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.953 INFO  CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:20:02.953 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
19:20:02.953 INFO  CountBasesInReference - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:20:02.953 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:20:02.953 INFO  CountBasesInReference - Start Date/Time: May 19, 2025 at 7:20:02 PM GMT
19:20:02.953 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.953 INFO  CountBasesInReference - ------------------------------------------------------------
19:20:02.953 INFO  CountBasesInReference - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:20:02.953 INFO  CountBasesInReference - Picard Version: 3.4.0
19:20:02.953 INFO  CountBasesInReference - Built for Spark Version: 3.5.0
19:20:02.953 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:20:02.953 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:20:02.954 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:20:02.954 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:20:02.954 INFO  CountBasesInReference - Deflater: IntelDeflater
19:20:02.954 INFO  CountBasesInReference - Inflater: IntelInflater
19:20:02.954 INFO  CountBasesInReference - GCS max retries/reopens: 20
19:20:02.954 INFO  CountBasesInReference - Requester pays: disabled
19:20:02.954 INFO  CountBasesInReference - Initializing engine
19:20:02.954 INFO  CountBasesInReference - Done initializing engine
19:20:02.954 INFO  ProgressMeter - Starting traversal
19:20:02.954 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
19:20:02.959 INFO  ProgressMeter -              4:16000              0.0                 64000      768000000.0
19:20:02.959 INFO  ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
19:20:02.960 INFO  CountBasesInReference - Shutting down engine
[May 19, 2025 at 7:20:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1738539008