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

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

tests

failures

ignored

0.083s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testCountBasesInReferenceFull	0.042s	passed
testCountBasesInReferenceWithInterval	0.015s	passed
testCountBasesInReferenceWithOutputFile	0.026s	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

16:56:03.010 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.010 INFO  CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:56:03.010 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
16:56:03.010 INFO  CountBasesInReference - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:56:03.010 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:56:03.010 INFO  CountBasesInReference - Start Date/Time: May 27, 2025 at 4:56:03 PM GMT
16:56:03.010 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.010 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.010 INFO  CountBasesInReference - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:56:03.010 INFO  CountBasesInReference - Picard Version: 3.4.0
16:56:03.010 INFO  CountBasesInReference - Built for Spark Version: 3.5.0
16:56:03.010 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:56:03.010 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:56:03.010 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:56:03.010 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:56:03.010 INFO  CountBasesInReference - Deflater: IntelDeflater
16:56:03.010 INFO  CountBasesInReference - Inflater: IntelInflater
16:56:03.010 INFO  CountBasesInReference - GCS max retries/reopens: 20
16:56:03.010 INFO  CountBasesInReference - Requester pays: disabled
16:56:03.010 INFO  CountBasesInReference - Initializing engine
16:56:03.011 INFO  CountBasesInReference - Done initializing engine
16:56:03.011 INFO  ProgressMeter - Starting traversal
16:56:03.011 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
16:56:03.037 INFO  ProgressMeter -              4:16000              0.0                 64000      147692307.7
16:56:03.038 INFO  ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
16:56:03.038 INFO  CountBasesInReference - Shutting down engine
[May 27, 2025 at 4:56:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1956642816
16:56:03.052 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.052 INFO  CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:56:03.052 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
16:56:03.052 INFO  CountBasesInReference - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:56:03.052 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:56:03.052 INFO  CountBasesInReference - Start Date/Time: May 27, 2025 at 4:56:03 PM GMT
16:56:03.052 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.052 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.052 INFO  CountBasesInReference - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:56:03.052 INFO  CountBasesInReference - Picard Version: 3.4.0
16:56:03.052 INFO  CountBasesInReference - Built for Spark Version: 3.5.0
16:56:03.052 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:56:03.052 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:56:03.052 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:56:03.052 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:56:03.052 INFO  CountBasesInReference - Deflater: IntelDeflater
16:56:03.052 INFO  CountBasesInReference - Inflater: IntelInflater
16:56:03.052 INFO  CountBasesInReference - GCS max retries/reopens: 20
16:56:03.052 INFO  CountBasesInReference - Requester pays: disabled
16:56:03.052 INFO  CountBasesInReference - Initializing engine
16:56:03.053 INFO  IntervalArgumentCollection - Processing 1001 bp from intervals
16:56:03.053 INFO  CountBasesInReference - Done initializing engine
16:56:03.053 INFO  ProgressMeter - Starting traversal
16:56:03.053 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
16:56:03.053 INFO  ProgressMeter -               1:5999              0.0                  1001         Infinity
16:56:03.053 INFO  ProgressMeter - Traversal complete. Processed 1001 total bases in 0.0 minutes.
16:56:03.053 INFO  CountBasesInReference - Shutting down engine
[May 27, 2025 at 4:56:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1956642816
16:56:03.067 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.067 INFO  CountBasesInReference - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:56:03.067 INFO  CountBasesInReference - For support and documentation go to https://software.broadinstitute.org/gatk/
16:56:03.067 INFO  CountBasesInReference - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:56:03.067 INFO  CountBasesInReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:56:03.067 INFO  CountBasesInReference - Start Date/Time: May 27, 2025 at 4:56:03 PM GMT
16:56:03.067 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.067 INFO  CountBasesInReference - ------------------------------------------------------------
16:56:03.067 INFO  CountBasesInReference - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:56:03.067 INFO  CountBasesInReference - Picard Version: 3.4.0
16:56:03.067 INFO  CountBasesInReference - Built for Spark Version: 3.5.0
16:56:03.067 INFO  CountBasesInReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:56:03.067 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:56:03.067 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:56:03.067 INFO  CountBasesInReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:56:03.067 INFO  CountBasesInReference - Deflater: IntelDeflater
16:56:03.067 INFO  CountBasesInReference - Inflater: IntelInflater
16:56:03.067 INFO  CountBasesInReference - GCS max retries/reopens: 20
16:56:03.067 INFO  CountBasesInReference - Requester pays: disabled
16:56:03.067 INFO  CountBasesInReference - Initializing engine
16:56:03.067 INFO  CountBasesInReference - Done initializing engine
16:56:03.068 INFO  ProgressMeter - Starting traversal
16:56:03.068 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
16:56:03.078 INFO  ProgressMeter -              4:16000              0.0                 64000      384000000.0
16:56:03.078 INFO  ProgressMeter - Traversal complete. Processed 64000 total bases in 0.0 minutes.
16:56:03.078 INFO  CountBasesInReference - Shutting down engine
[May 27, 2025 at 4:56:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1956642816