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

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

tests
0

failures
0

ignored
1m2.42s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.090s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.090s passed
testBQSRFailWithoutDBSNP 0.083s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 6.751s 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 ')) 2.713s 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')) 0.690s 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')) 0.750s 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')) 0.723s 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')) 0.701s 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')) 1.073s 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')) 0.167s 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')) 8.244s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.173s 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')) 0.250s 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')) 8.940s 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')) 8.079s 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')) 8.104s 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')) 12.471s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.734s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.699s passed
testPlottingWorkflow 0.895s passed

Standard output

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[15:14:59] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[15:15:06] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[15:15:14] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[15:15:14] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[15:15:15] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[15:15:24] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[15:15:32] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[15:15:40] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[15:15:52] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[15:15:53] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[15:15:54] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[15:15:56] 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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[15:15:57] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[15:15:58] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[15:15:59] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[15:15:59] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[15:16:00] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[15:16:01] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[15:16:01] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[15:16:01] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[May 27, 2025 at 3:15:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:15:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:16:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:16:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:16:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 27, 2025 at 3:16:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
15:16:01.331 INFO  BaseRecalibrator - ------------------------------------------------------------
15:16:01.331 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:16:01.331 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:16:01.331 INFO  BaseRecalibrator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:16:01.331 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:16:01.331 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 3:16:01 PM GMT
15:16:01.331 INFO  BaseRecalibrator - ------------------------------------------------------------
15:16:01.331 INFO  BaseRecalibrator - ------------------------------------------------------------
15:16:01.331 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:16:01.332 INFO  BaseRecalibrator - Picard Version: 3.4.0
15:16:01.332 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
15:16:01.332 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:16:01.332 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:16:01.332 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:16:01.332 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:16:01.332 INFO  BaseRecalibrator - Deflater: IntelDeflater
15:16:01.332 INFO  BaseRecalibrator - Inflater: IntelInflater
15:16:01.332 INFO  BaseRecalibrator - GCS max retries/reopens: 20
15:16:01.332 INFO  BaseRecalibrator - Requester pays: disabled
15:16:01.332 INFO  BaseRecalibrator - Initializing engine
15:16:01.333 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
15:16:01.334 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
15:16:01.334 INFO  BaseRecalibrator - Done initializing engine
15:16:01.340 INFO  BaseRecalibrationEngine - The covariates being used here: 
15:16:01.340 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
15:16:01.340 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
15:16:01.340 INFO  BaseRecalibrationEngine - 	ContextCovariate
15:16:01.341 INFO  BaseRecalibrationEngine - 	CycleCovariate
15:16:01.341 INFO  ProgressMeter - Starting traversal
15:16:01.341 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
15:16:01.353 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
15:16:01.353 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
15:16:01.353 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
15:16:01.354 INFO  BaseRecalibrator - Calculating quantized quality scores...
15:16:01.355 INFO  BaseRecalibrator - Writing recalibration report...
15:16:01.942 INFO  BaseRecalibrator - ...done!
15:16:01.942 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
15:16:01.942 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 3:16:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
15:16:01.959 INFO  ApplyBQSR - ------------------------------------------------------------
15:16:01.959 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:16:01.959 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
15:16:01.959 INFO  ApplyBQSR - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:16:01.959 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:16:01.959 INFO  ApplyBQSR - Start Date/Time: May 27, 2025 at 3:16:01 PM GMT
15:16:01.959 INFO  ApplyBQSR - ------------------------------------------------------------
15:16:01.959 INFO  ApplyBQSR - ------------------------------------------------------------
15:16:01.959 INFO  ApplyBQSR - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:16:01.959 INFO  ApplyBQSR - Picard Version: 3.4.0
15:16:01.959 INFO  ApplyBQSR - Built for Spark Version: 3.5.0
15:16:01.959 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:16:01.959 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:16:01.959 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:16:01.959 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:16:01.959 INFO  ApplyBQSR - Deflater: IntelDeflater
15:16:01.959 INFO  ApplyBQSR - Inflater: IntelInflater
15:16:01.959 INFO  ApplyBQSR - GCS max retries/reopens: 20
15:16:01.959 INFO  ApplyBQSR - Requester pays: disabled
15:16:01.959 INFO  ApplyBQSR - Initializing engine
15:16:01.960 INFO  ApplyBQSR - Done initializing engine
15:16:01.960 INFO  ProgressMeter - Starting traversal
15:16:01.960 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
15:16:02.011 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

15:16:02.011 INFO  ProgressMeter -             unmapped              0.0                   493         580000.0
15:16:02.011 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
15:16:02.062 INFO  ApplyBQSR - Shutting down engine
[May 27, 2025 at 3:16:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
15:16:02.075 INFO  BaseRecalibrator - ------------------------------------------------------------
15:16:02.075 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g93cf621-SNAPSHOT
15:16:02.075 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:16:02.075 INFO  BaseRecalibrator - Executing as root@07a40c7a9995 on Linux v6.11.0-1014-azure amd64
15:16:02.075 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:16:02.075 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 3:16:02 PM GMT
15:16:02.075 INFO  BaseRecalibrator - ------------------------------------------------------------
15:16:02.075 INFO  BaseRecalibrator - ------------------------------------------------------------
15:16:02.075 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
15:16:02.075 INFO  BaseRecalibrator - Picard Version: 3.4.0
15:16:02.075 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
15:16:02.075 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:16:02.075 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:16:02.075 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:16:02.075 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:16:02.075 INFO  BaseRecalibrator - Deflater: IntelDeflater
15:16:02.075 INFO  BaseRecalibrator - Inflater: IntelInflater
15:16:02.075 INFO  BaseRecalibrator - GCS max retries/reopens: 20
15:16:02.075 INFO  BaseRecalibrator - Requester pays: disabled
15:16:02.075 INFO  BaseRecalibrator - Initializing engine
15:16:02.077 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
15:16:02.078 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
15:16:02.078 INFO  BaseRecalibrator - Done initializing engine
15:16:02.085 INFO  BaseRecalibrationEngine - The covariates being used here: 
15:16:02.085 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
15:16:02.086 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
15:16:02.086 INFO  BaseRecalibrationEngine - 	ContextCovariate
15:16:02.086 INFO  BaseRecalibrationEngine - 	CycleCovariate
15:16:02.086 INFO  ProgressMeter - Starting traversal
15:16:02.086 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
15:16:02.102 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
15:16:02.102 INFO  ProgressMeter -             unmapped              0.0                   373        1398750.0
15:16:02.102 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
15:16:02.102 INFO  BaseRecalibrator - Calculating quantized quality scores...
15:16:02.103 INFO  BaseRecalibrator - Writing recalibration report...
15:16:02.202 INFO  BaseRecalibrator - ...done!
15:16:02.202 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
15:16:02.202 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 3:16:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
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