Class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibratorIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.bqsr > BaseRecalibratorIntegrationTest
21

tests
0

failures
0

ignored
1m2.93s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.093s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.087s passed
testBQSRFailWithoutDBSNP 0.086s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 6.681s passed
testBQSR[10](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.4379150-4379157.bam', args='-indels --enable-baq ')) 2.728s passed
testBQSR[11](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf')) 0.759s passed
testBQSR[12](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --indels-context-size 4')) 0.798s passed
testBQSR[13](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --low-quality-tail 5')) 0.745s passed
testBQSR[14](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --quantizing-levels 6')) 0.743s passed
testBQSR[15](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --mismatches-context-size 4')) 1.117s passed
testBQSR[16](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/originalQuals.1kg.chr1.1-1K.1RG.dictFix.bam', args='-indels --enable-baq -OQ')) 0.223s passed
testBQSR[1](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq')) 8.108s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.224s passed
testBQSR[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.oq.read_consumes_zero_ref_bases.chr20.bam', args='-indels --enable-baq')) 0.299s passed
testBQSR[4](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --indels-context-size 4')) 8.942s passed
testBQSR[5](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --low-quality-tail 5')) 8.209s passed
testBQSR[6](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --quantizing-levels 6')) 8.057s passed
testBQSR[7](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --mismatches-context-size 4')) 12.330s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.765s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.756s passed
testPlottingWorkflow 1.182s passed

Standard output

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[21:03:28] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[21:03:35] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[21:03:43] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[21:03:43] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[21:03:44] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[21:03:53] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[21:04:01] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[21:04:09] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[21:04:21] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[21:04:22] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[21:04:23] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[21:04:25] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf
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[21:04:26] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[21:04:27] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[21:04:28] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[21:04:28] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[21:04:30] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[21:04:30] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[21:04:30] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[21:04:30] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[June 12, 2025 at 9:03:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:03:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:03:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:03:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:03:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1382023168
[June 12, 2025 at 9:04:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1382023168
21:04:30.557 INFO  BaseRecalibrator - ------------------------------------------------------------
21:04:30.557 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:04:30.557 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
21:04:30.557 INFO  BaseRecalibrator - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:04:30.557 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:04:30.557 INFO  BaseRecalibrator - Start Date/Time: June 12, 2025 at 9:04:30 PM GMT
21:04:30.557 INFO  BaseRecalibrator - ------------------------------------------------------------
21:04:30.557 INFO  BaseRecalibrator - ------------------------------------------------------------
21:04:30.557 INFO  BaseRecalibrator - HTSJDK Version: 4.2.0
21:04:30.557 INFO  BaseRecalibrator - Picard Version: 3.4.0
21:04:30.557 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
21:04:30.557 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:04:30.557 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:04:30.557 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:04:30.557 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:04:30.557 INFO  BaseRecalibrator - Deflater: IntelDeflater
21:04:30.557 INFO  BaseRecalibrator - Inflater: IntelInflater
21:04:30.557 INFO  BaseRecalibrator - GCS max retries/reopens: 20
21:04:30.557 INFO  BaseRecalibrator - Requester pays: disabled
21:04:30.557 INFO  BaseRecalibrator - Initializing engine
21:04:30.559 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf
21:04:30.560 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
21:04:30.560 INFO  BaseRecalibrator - Done initializing engine
21:04:30.613 INFO  Reflections - Reflections took 47 ms to scan 3 urls, producing 7 keys and 18 values 
21:04:30.614 INFO  BaseRecalibrationEngine - The covariates being used here: 
21:04:30.614 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
21:04:30.614 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
21:04:30.614 INFO  BaseRecalibrationEngine - 	ContextCovariate
21:04:30.614 INFO  BaseRecalibrationEngine - 	CycleCovariate
21:04:30.614 INFO  ProgressMeter - Starting traversal
21:04:30.614 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:04:30.626 INFO  BaseRecalibrator - 14 read(s) filtered by: MappingQualityNotZeroReadFilter 
0 read(s) filtered by: MappingQualityAvailableReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 read(s) filtered by: NotSecondaryAlignmentReadFilter 
59 read(s) filtered by: NotDuplicateReadFilter 
47 read(s) filtered by: PassesVendorQualityCheckReadFilter 
0 read(s) filtered by: WellformedReadFilter 
120 total reads filtered out of 493 reads processed
21:04:30.626 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
21:04:30.626 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
21:04:30.627 INFO  BaseRecalibrator - Calculating quantized quality scores...
21:04:30.628 INFO  BaseRecalibrator - Writing recalibration report...
21:04:31.207 INFO  BaseRecalibrator - ...done!
21:04:31.207 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
21:04:31.207 INFO  BaseRecalibrator - Shutting down engine
[June 12, 2025 at 9:04:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1382023168
21:04:31.221 INFO  ApplyBQSR - ------------------------------------------------------------
21:04:31.221 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:04:31.221 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
21:04:31.221 INFO  ApplyBQSR - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:04:31.221 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:04:31.221 INFO  ApplyBQSR - Start Date/Time: June 12, 2025 at 9:04:31 PM GMT
21:04:31.221 INFO  ApplyBQSR - ------------------------------------------------------------
21:04:31.221 INFO  ApplyBQSR - ------------------------------------------------------------
21:04:31.221 INFO  ApplyBQSR - HTSJDK Version: 4.2.0
21:04:31.221 INFO  ApplyBQSR - Picard Version: 3.4.0
21:04:31.221 INFO  ApplyBQSR - Built for Spark Version: 3.5.0
21:04:31.221 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:04:31.221 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:04:31.221 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:04:31.221 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:04:31.221 INFO  ApplyBQSR - Deflater: IntelDeflater
21:04:31.221 INFO  ApplyBQSR - Inflater: IntelInflater
21:04:31.221 INFO  ApplyBQSR - GCS max retries/reopens: 20
21:04:31.221 INFO  ApplyBQSR - Requester pays: disabled
21:04:31.221 INFO  ApplyBQSR - Initializing engine
21:04:31.222 INFO  ApplyBQSR - Done initializing engine
21:04:31.284 INFO  Reflections - Reflections took 50 ms to scan 3 urls, producing 7 keys and 18 values 
21:04:31.332 INFO  Reflections - Reflections took 48 ms to scan 3 urls, producing 7 keys and 18 values 
21:04:31.332 WARN  BQSRCovariateList - Covariate ReadGroupCovariate is a required covariate that is always on. Ignoring explicit request for it.
21:04:31.332 WARN  BQSRCovariateList - Covariate QualityScoreCovariate is a required covariate that is always on. Ignoring explicit request for it.
21:04:31.332 WARN  BQSRCovariateList - Covariate ContextCovariate is a standard covariate that is always on when not running with --no-standard-covariates. Ignoring explicit request for it.
21:04:31.332 WARN  BQSRCovariateList - Covariate CycleCovariate is a standard covariate that is always on when not running with --no-standard-covariates. Ignoring explicit request for it.
21:04:31.339 INFO  ApplyBQSR - Loaded covariates ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate from recalibration table /tmp/local18970223784451453307/gatk4.pre.cols8972360238648229222.table
21:04:31.339 INFO  ProgressMeter - Starting traversal
21:04:31.339 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:04:31.398 INFO  Reflections - Reflections took 47 ms to scan 3 urls, producing 7 keys and 18 values 
21:04:31.446 INFO  Reflections - Reflections took 47 ms to scan 3 urls, producing 7 keys and 18 values 
21:04:31.446 WARN  BQSRCovariateList - Covariate ReadGroupCovariate is a required covariate that is always on. Ignoring explicit request for it.
21:04:31.447 WARN  BQSRCovariateList - Covariate QualityScoreCovariate is a required covariate that is always on. Ignoring explicit request for it.
21:04:31.447 WARN  BQSRCovariateList - Covariate ContextCovariate is a standard covariate that is always on when not running with --no-standard-covariates. Ignoring explicit request for it.
21:04:31.447 WARN  BQSRCovariateList - Covariate CycleCovariate is a standard covariate that is always on when not running with --no-standard-covariates. Ignoring explicit request for it.
21:04:31.484 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

21:04:31.484 INFO  ProgressMeter -             unmapped              0.0                   493         204000.0
21:04:31.484 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
21:04:31.535 INFO  ApplyBQSR - Shutting down engine
[June 12, 2025 at 9:04:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1382023168
21:04:31.549 INFO  BaseRecalibrator - ------------------------------------------------------------
21:04:31.549 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-8-g092bdf2-SNAPSHOT
21:04:31.549 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
21:04:31.549 INFO  BaseRecalibrator - Executing as root@e24cea241624 on Linux v6.11.0-1015-azure amd64
21:04:31.549 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:04:31.549 INFO  BaseRecalibrator - Start Date/Time: June 12, 2025 at 9:04:31 PM GMT
21:04:31.549 INFO  BaseRecalibrator - ------------------------------------------------------------
21:04:31.549 INFO  BaseRecalibrator - ------------------------------------------------------------
21:04:31.549 INFO  BaseRecalibrator - HTSJDK Version: 4.2.0
21:04:31.549 INFO  BaseRecalibrator - Picard Version: 3.4.0
21:04:31.549 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
21:04:31.549 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:04:31.549 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:04:31.549 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:04:31.549 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:04:31.549 INFO  BaseRecalibrator - Deflater: IntelDeflater
21:04:31.549 INFO  BaseRecalibrator - Inflater: IntelInflater
21:04:31.549 INFO  BaseRecalibrator - GCS max retries/reopens: 20
21:04:31.549 INFO  BaseRecalibrator - Requester pays: disabled
21:04:31.549 INFO  BaseRecalibrator - Initializing engine
21:04:31.550 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf
21:04:31.551 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
21:04:31.551 INFO  BaseRecalibrator - Done initializing engine
21:04:31.605 INFO  Reflections - Reflections took 48 ms to scan 3 urls, producing 7 keys and 18 values 
21:04:31.605 INFO  BaseRecalibrationEngine - The covariates being used here: 
21:04:31.605 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
21:04:31.605 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
21:04:31.605 INFO  BaseRecalibrationEngine - 	ContextCovariate
21:04:31.605 INFO  BaseRecalibrationEngine - 	CycleCovariate
21:04:31.605 INFO  ProgressMeter - Starting traversal
21:04:31.605 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
21:04:31.616 INFO  BaseRecalibrator - 14 read(s) filtered by: MappingQualityNotZeroReadFilter 
0 read(s) filtered by: MappingQualityAvailableReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 read(s) filtered by: NotSecondaryAlignmentReadFilter 
59 read(s) filtered by: NotDuplicateReadFilter 
47 read(s) filtered by: PassesVendorQualityCheckReadFilter 
0 read(s) filtered by: WellformedReadFilter 
120 total reads filtered out of 493 reads processed
21:04:31.616 INFO  ProgressMeter -             unmapped              0.0                   373        2034545.5
21:04:31.616 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
21:04:31.616 INFO  BaseRecalibrator - Calculating quantized quality scores...
21:04:31.617 INFO  BaseRecalibrator - Writing recalibration report...
21:04:31.714 INFO  BaseRecalibrator - ...done!
21:04:31.714 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
21:04:31.714 INFO  BaseRecalibrator - Shutting down engine
[June 12, 2025 at 9:04:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1382023168
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, The unaligned mate start position is 69400, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 130, Read name 809R9ABXX101220:5:6:17918:145992, The unaligned mate start position is 69400, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, The unaligned mate start position is 69471, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 275, Read name 809R9ABXX101220:5:8:7119:101555, The unaligned mate start position is 69471, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, The unaligned mate start position is 69569, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 419, Read name 809R9ABXX101220:5:48:20204:50350, The unaligned mate start position is 69569, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0