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

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

tests
0

failures
0

ignored
1m3.59s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.105s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.103s passed
testBQSRFailWithoutDBSNP 0.100s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 6.848s 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 ')) 2.764s 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')) 0.760s 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')) 0.791s 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')) 0.761s 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')) 0.764s 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')) 1.136s 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')) 0.198s 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')) 8.262s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.195s 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')) 0.290s 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')) 9.168s 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')) 8.145s 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')) 8.235s 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')) 12.525s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.752s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.743s passed
testPlottingWorkflow 0.944s passed

Standard output

--------------------------------------------------------------------------------
[18:35:05] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[18:35:11] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[18:35:20] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[18:35:20] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[18:35:20] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[18:35:29] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[18:35:38] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[18:35:46] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[18:35:58] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[18:35:59] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[18:36:00] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[18:36:03] 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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[18:36:03] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[18:36:04] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[18:36:05] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[18:36:06] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[18:36:07] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[18:36:07] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[18:36:07] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[18:36:07] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[May 27, 2025 at 6:35:11 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:35:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:35:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:35:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:35:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:35:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:35:46 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:35:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:35:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:36:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
18:36:07.800 INFO  BaseRecalibrator - ------------------------------------------------------------
18:36:07.800 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:36:07.800 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:36:07.800 INFO  BaseRecalibrator - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:36:07.800 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:36:07.800 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 6:36:07 PM GMT
18:36:07.800 INFO  BaseRecalibrator - ------------------------------------------------------------
18:36:07.800 INFO  BaseRecalibrator - ------------------------------------------------------------
18:36:07.800 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:36:07.800 INFO  BaseRecalibrator - Picard Version: 3.4.0
18:36:07.800 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
18:36:07.800 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:36:07.800 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:36:07.800 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:36:07.800 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:36:07.800 INFO  BaseRecalibrator - Deflater: IntelDeflater
18:36:07.800 INFO  BaseRecalibrator - Inflater: IntelInflater
18:36:07.800 INFO  BaseRecalibrator - GCS max retries/reopens: 20
18:36:07.800 INFO  BaseRecalibrator - Requester pays: disabled
18:36:07.800 INFO  BaseRecalibrator - Initializing engine
18:36:07.802 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
18:36:07.803 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
18:36:07.803 INFO  BaseRecalibrator - Done initializing engine
18:36:07.811 INFO  BaseRecalibrationEngine - The covariates being used here: 
18:36:07.811 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
18:36:07.811 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
18:36:07.811 INFO  BaseRecalibrationEngine - 	ContextCovariate
18:36:07.811 INFO  BaseRecalibrationEngine - 	CycleCovariate
18:36:07.811 INFO  ProgressMeter - Starting traversal
18:36:07.811 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
18:36:07.826 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
18:36:07.826 INFO  ProgressMeter -             unmapped              0.0                   373        1492000.0
18:36:07.826 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
18:36:07.826 INFO  BaseRecalibrator - Calculating quantized quality scores...
18:36:07.828 INFO  BaseRecalibrator - Writing recalibration report...
18:36:08.449 INFO  BaseRecalibrator - ...done!
18:36:08.449 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
18:36:08.449 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 6:36:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160
18:36:08.465 INFO  ApplyBQSR - ------------------------------------------------------------
18:36:08.465 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:36:08.465 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
18:36:08.465 INFO  ApplyBQSR - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:36:08.465 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:36:08.465 INFO  ApplyBQSR - Start Date/Time: May 27, 2025 at 6:36:08 PM GMT
18:36:08.465 INFO  ApplyBQSR - ------------------------------------------------------------
18:36:08.465 INFO  ApplyBQSR - ------------------------------------------------------------
18:36:08.465 INFO  ApplyBQSR - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:36:08.465 INFO  ApplyBQSR - Picard Version: 3.4.0
18:36:08.465 INFO  ApplyBQSR - Built for Spark Version: 3.5.0
18:36:08.465 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:36:08.465 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:36:08.465 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:36:08.465 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:36:08.465 INFO  ApplyBQSR - Deflater: IntelDeflater
18:36:08.465 INFO  ApplyBQSR - Inflater: IntelInflater
18:36:08.465 INFO  ApplyBQSR - GCS max retries/reopens: 20
18:36:08.465 INFO  ApplyBQSR - Requester pays: disabled
18:36:08.465 INFO  ApplyBQSR - Initializing engine
18:36:08.466 INFO  ApplyBQSR - Done initializing engine
18:36:08.467 INFO  ProgressMeter - Starting traversal
18:36:08.467 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
18:36:08.520 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

18:36:08.520 INFO  ProgressMeter -             unmapped              0.0                   493         558113.2
18:36:08.520 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
18:36:08.570 INFO  ApplyBQSR - Shutting down engine
[May 27, 2025 at 6:36:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
18:36:08.587 INFO  BaseRecalibrator - ------------------------------------------------------------
18:36:08.587 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g06789f4-SNAPSHOT
18:36:08.587 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:36:08.587 INFO  BaseRecalibrator - Executing as root@9bb9f17fa524 on Linux v6.11.0-1014-azure amd64
18:36:08.587 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
18:36:08.587 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 6:36:08 PM GMT
18:36:08.587 INFO  BaseRecalibrator - ------------------------------------------------------------
18:36:08.587 INFO  BaseRecalibrator - ------------------------------------------------------------
18:36:08.587 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
18:36:08.587 INFO  BaseRecalibrator - Picard Version: 3.4.0
18:36:08.587 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
18:36:08.587 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:36:08.587 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:36:08.587 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:36:08.587 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:36:08.587 INFO  BaseRecalibrator - Deflater: IntelDeflater
18:36:08.587 INFO  BaseRecalibrator - Inflater: IntelInflater
18:36:08.587 INFO  BaseRecalibrator - GCS max retries/reopens: 20
18:36:08.587 INFO  BaseRecalibrator - Requester pays: disabled
18:36:08.587 INFO  BaseRecalibrator - Initializing engine
18:36:08.589 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
18:36:08.590 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
18:36:08.590 INFO  BaseRecalibrator - Done initializing engine
18:36:08.598 INFO  BaseRecalibrationEngine - The covariates being used here: 
18:36:08.598 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
18:36:08.598 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
18:36:08.598 INFO  BaseRecalibrationEngine - 	ContextCovariate
18:36:08.598 INFO  BaseRecalibrationEngine - 	CycleCovariate
18:36:08.599 INFO  ProgressMeter - Starting traversal
18:36:08.599 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
18:36:08.611 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
18:36:08.611 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
18:36:08.611 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
18:36:08.611 INFO  BaseRecalibrator - Calculating quantized quality scores...
18:36:08.612 INFO  BaseRecalibrator - Writing recalibration report...
18:36:08.716 INFO  BaseRecalibrator - ...done!
18:36:08.716 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
18:36:08.716 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 6:36:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
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