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

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

tests
0

failures
0

ignored
1m1.96s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.094s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.086s passed
testBQSRFailWithoutDBSNP 0.094s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 6.693s 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 ')) 2.676s 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')) 0.697s 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')) 0.751s 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')) 0.689s 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')) 0.706s 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')) 1.070s 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')) 0.171s 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')) 8.293s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.180s 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')) 0.251s 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')) 8.917s 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')) 7.923s 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')) 8.098s 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')) 12.273s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.729s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.691s passed
testPlottingWorkflow 0.875s passed

Standard output

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[14:38:40] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[14:38:47] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[14:38:55] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[14:38:55] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[14:38:56] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[14:39:04] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[14:39:12] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[14:39:20] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[14:39:33] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[14:39:33] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[14:39:34] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[14:39:37] 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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[14:39:38] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[14:39:38] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[14:39:39] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[14:39:40] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[14:39:41] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[14:39:41] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[14:39:41] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[14:39:41] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[June 2, 2025 at 2:38:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:38:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:38:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:38:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1327497216
[June 2, 2025 at 2:39:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1327497216
14:39:41.716 INFO  BaseRecalibrator - ------------------------------------------------------------
14:39:41.717 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:39:41.717 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:39:41.717 INFO  BaseRecalibrator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:39:41.717 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:39:41.717 INFO  BaseRecalibrator - Start Date/Time: June 2, 2025 at 2:39:41 PM GMT
14:39:41.717 INFO  BaseRecalibrator - ------------------------------------------------------------
14:39:41.717 INFO  BaseRecalibrator - ------------------------------------------------------------
14:39:41.717 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:39:41.717 INFO  BaseRecalibrator - Picard Version: 3.4.0
14:39:41.717 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
14:39:41.717 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:39:41.717 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:39:41.717 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:39:41.717 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:39:41.717 INFO  BaseRecalibrator - Deflater: IntelDeflater
14:39:41.717 INFO  BaseRecalibrator - Inflater: IntelInflater
14:39:41.717 INFO  BaseRecalibrator - GCS max retries/reopens: 20
14:39:41.717 INFO  BaseRecalibrator - Requester pays: disabled
14:39:41.717 INFO  BaseRecalibrator - Initializing engine
14:39:41.718 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
14:39:41.719 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
14:39:41.719 INFO  BaseRecalibrator - Done initializing engine
14:39:41.726 INFO  BaseRecalibrationEngine - The covariates being used here: 
14:39:41.726 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
14:39:41.726 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
14:39:41.726 INFO  BaseRecalibrationEngine - 	ContextCovariate
14:39:41.726 INFO  BaseRecalibrationEngine - 	CycleCovariate
14:39:41.726 INFO  ProgressMeter - Starting traversal
14:39:41.726 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
14:39:41.738 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
14:39:41.738 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
14:39:41.738 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
14:39:41.739 INFO  BaseRecalibrator - Calculating quantized quality scores...
14:39:41.741 INFO  BaseRecalibrator - Writing recalibration report...
14:39:42.319 INFO  BaseRecalibrator - ...done!
14:39:42.319 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
14:39:42.319 INFO  BaseRecalibrator - Shutting down engine
[June 2, 2025 at 2:39:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1327497216
14:39:42.332 INFO  ApplyBQSR - ------------------------------------------------------------
14:39:42.333 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:39:42.333 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
14:39:42.333 INFO  ApplyBQSR - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:39:42.333 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:39:42.333 INFO  ApplyBQSR - Start Date/Time: June 2, 2025 at 2:39:42 PM GMT
14:39:42.333 INFO  ApplyBQSR - ------------------------------------------------------------
14:39:42.333 INFO  ApplyBQSR - ------------------------------------------------------------
14:39:42.333 INFO  ApplyBQSR - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:39:42.333 INFO  ApplyBQSR - Picard Version: 3.4.0
14:39:42.333 INFO  ApplyBQSR - Built for Spark Version: 3.5.0
14:39:42.333 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:39:42.333 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:39:42.333 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:39:42.333 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:39:42.333 INFO  ApplyBQSR - Deflater: IntelDeflater
14:39:42.333 INFO  ApplyBQSR - Inflater: IntelInflater
14:39:42.333 INFO  ApplyBQSR - GCS max retries/reopens: 20
14:39:42.333 INFO  ApplyBQSR - Requester pays: disabled
14:39:42.333 INFO  ApplyBQSR - Initializing engine
14:39:42.333 INFO  ApplyBQSR - Done initializing engine
14:39:42.334 INFO  ProgressMeter - Starting traversal
14:39:42.334 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
14:39:42.387 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

14:39:42.387 INFO  ProgressMeter -             unmapped              0.0                   493         558113.2
14:39:42.387 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
14:39:42.438 INFO  ApplyBQSR - Shutting down engine
[June 2, 2025 at 2:39:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1327497216
14:39:42.451 INFO  BaseRecalibrator - ------------------------------------------------------------
14:39:42.451 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-7-g5749ecb-SNAPSHOT
14:39:42.451 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:39:42.451 INFO  BaseRecalibrator - Executing as root@7f71e7f19701 on Linux v6.11.0-1014-azure amd64
14:39:42.452 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
14:39:42.452 INFO  BaseRecalibrator - Start Date/Time: June 2, 2025 at 2:39:42 PM GMT
14:39:42.452 INFO  BaseRecalibrator - ------------------------------------------------------------
14:39:42.452 INFO  BaseRecalibrator - ------------------------------------------------------------
14:39:42.452 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
14:39:42.452 INFO  BaseRecalibrator - Picard Version: 3.4.0
14:39:42.452 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
14:39:42.452 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:39:42.452 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:39:42.452 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:39:42.452 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:39:42.452 INFO  BaseRecalibrator - Deflater: IntelDeflater
14:39:42.452 INFO  BaseRecalibrator - Inflater: IntelInflater
14:39:42.452 INFO  BaseRecalibrator - GCS max retries/reopens: 20
14:39:42.452 INFO  BaseRecalibrator - Requester pays: disabled
14:39:42.452 INFO  BaseRecalibrator - Initializing engine
14:39:42.453 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
14:39:42.454 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
14:39:42.454 INFO  BaseRecalibrator - Done initializing engine
14:39:42.460 INFO  BaseRecalibrationEngine - The covariates being used here: 
14:39:42.460 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
14:39:42.460 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
14:39:42.460 INFO  BaseRecalibrationEngine - 	ContextCovariate
14:39:42.460 INFO  BaseRecalibrationEngine - 	CycleCovariate
14:39:42.460 INFO  ProgressMeter - Starting traversal
14:39:42.460 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
14:39:42.471 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
14:39:42.471 INFO  ProgressMeter -             unmapped              0.0                   373        2034545.5
14:39:42.471 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
14:39:42.471 INFO  BaseRecalibrator - Calculating quantized quality scores...
14:39:42.472 INFO  BaseRecalibrator - Writing recalibration report...
14:39:42.569 INFO  BaseRecalibrator - ...done!
14:39:42.569 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
14:39:42.569 INFO  BaseRecalibrator - Shutting down engine
[June 2, 2025 at 2:39:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1327497216
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