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

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

tests
0

failures
0

ignored
1m1.66s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.088s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.085s 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='')) 6.681s 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 ')) 2.669s 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')) 0.691s 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')) 0.692s 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')) 1.065s 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')) 0.173s 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')) 8.266s 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')) 0.253s 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')) 8.854s 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')) 7.958s 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')) 7.935s 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')) 12.231s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.722s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.694s passed
testPlottingWorkflow 0.884s passed

Standard output

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[16:03:21] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[16:03:28] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[16:03:36] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[16:03:36] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[16:03:37] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[16:03:46] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[16:03:54] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[16:04:01] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[16:04:14] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[16:04:14] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[16:04:15] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[16:04:18] 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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[16:04:18] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[16:04:19] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[16:04:20] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[16:04:21] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[16:04:22] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[16:04:22] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[16:04:22] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[16:04:22] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[May 27, 2025 at 4:03:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:03:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:03:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:03:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:03:46 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:03:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1568669696
[May 27, 2025 at 4:04:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1568669696
16:04:22.618 INFO  BaseRecalibrator - ------------------------------------------------------------
16:04:22.618 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
16:04:22.618 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:04:22.618 INFO  BaseRecalibrator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
16:04:22.618 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:04:22.618 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 4:04:22 PM GMT
16:04:22.618 INFO  BaseRecalibrator - ------------------------------------------------------------
16:04:22.618 INFO  BaseRecalibrator - ------------------------------------------------------------
16:04:22.618 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:04:22.618 INFO  BaseRecalibrator - Picard Version: 3.4.0
16:04:22.618 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
16:04:22.618 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:04:22.618 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:04:22.618 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:04:22.618 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:04:22.618 INFO  BaseRecalibrator - Deflater: IntelDeflater
16:04:22.618 INFO  BaseRecalibrator - Inflater: IntelInflater
16:04:22.618 INFO  BaseRecalibrator - GCS max retries/reopens: 20
16:04:22.618 INFO  BaseRecalibrator - Requester pays: disabled
16:04:22.618 INFO  BaseRecalibrator - Initializing engine
16:04:22.620 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
16:04:22.620 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
16:04:22.620 INFO  BaseRecalibrator - Done initializing engine
16:04:22.626 INFO  BaseRecalibrationEngine - The covariates being used here: 
16:04:22.626 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
16:04:22.626 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
16:04:22.626 INFO  BaseRecalibrationEngine - 	ContextCovariate
16:04:22.626 INFO  BaseRecalibrationEngine - 	CycleCovariate
16:04:22.627 INFO  ProgressMeter - Starting traversal
16:04:22.627 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:04:22.644 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
16:04:22.644 INFO  ProgressMeter -             unmapped              0.0                   373        1316470.6
16:04:22.644 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
16:04:22.645 INFO  BaseRecalibrator - Calculating quantized quality scores...
16:04:22.647 INFO  BaseRecalibrator - Writing recalibration report...
16:04:23.222 INFO  BaseRecalibrator - ...done!
16:04:23.222 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
16:04:23.223 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 4:04:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1568669696
16:04:23.242 INFO  ApplyBQSR - ------------------------------------------------------------
16:04:23.242 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
16:04:23.242 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
16:04:23.242 INFO  ApplyBQSR - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
16:04:23.242 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:04:23.242 INFO  ApplyBQSR - Start Date/Time: May 27, 2025 at 4:04:23 PM GMT
16:04:23.242 INFO  ApplyBQSR - ------------------------------------------------------------
16:04:23.242 INFO  ApplyBQSR - ------------------------------------------------------------
16:04:23.242 INFO  ApplyBQSR - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:04:23.242 INFO  ApplyBQSR - Picard Version: 3.4.0
16:04:23.242 INFO  ApplyBQSR - Built for Spark Version: 3.5.0
16:04:23.242 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:04:23.242 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:04:23.242 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:04:23.242 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:04:23.242 INFO  ApplyBQSR - Deflater: IntelDeflater
16:04:23.242 INFO  ApplyBQSR - Inflater: IntelInflater
16:04:23.242 INFO  ApplyBQSR - GCS max retries/reopens: 20
16:04:23.242 INFO  ApplyBQSR - Requester pays: disabled
16:04:23.242 INFO  ApplyBQSR - Initializing engine
16:04:23.243 INFO  ApplyBQSR - Done initializing engine
16:04:23.243 INFO  ProgressMeter - Starting traversal
16:04:23.243 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:04:23.296 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

16:04:23.296 INFO  ProgressMeter -             unmapped              0.0                   493         558113.2
16:04:23.296 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
16:04:23.346 INFO  ApplyBQSR - Shutting down engine
[May 27, 2025 at 4:04:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1568669696
16:04:23.361 INFO  BaseRecalibrator - ------------------------------------------------------------
16:04:23.361 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-gf5385f1-SNAPSHOT
16:04:23.361 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:04:23.361 INFO  BaseRecalibrator - Executing as root@1be272c3efa7 on Linux v6.11.0-1014-azure amd64
16:04:23.361 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:04:23.361 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 4:04:23 PM GMT
16:04:23.361 INFO  BaseRecalibrator - ------------------------------------------------------------
16:04:23.361 INFO  BaseRecalibrator - ------------------------------------------------------------
16:04:23.361 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:04:23.361 INFO  BaseRecalibrator - Picard Version: 3.4.0
16:04:23.361 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
16:04:23.361 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:04:23.361 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:04:23.361 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:04:23.361 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:04:23.361 INFO  BaseRecalibrator - Deflater: IntelDeflater
16:04:23.361 INFO  BaseRecalibrator - Inflater: IntelInflater
16:04:23.361 INFO  BaseRecalibrator - GCS max retries/reopens: 20
16:04:23.361 INFO  BaseRecalibrator - Requester pays: disabled
16:04:23.361 INFO  BaseRecalibrator - Initializing engine
16:04:23.362 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
16:04:23.363 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
16:04:23.363 INFO  BaseRecalibrator - Done initializing engine
16:04:23.369 INFO  BaseRecalibrationEngine - The covariates being used here: 
16:04:23.369 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
16:04:23.369 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
16:04:23.369 INFO  BaseRecalibrationEngine - 	ContextCovariate
16:04:23.369 INFO  BaseRecalibrationEngine - 	CycleCovariate
16:04:23.370 INFO  ProgressMeter - Starting traversal
16:04:23.370 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:04:23.380 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
16:04:23.380 INFO  ProgressMeter -             unmapped              0.0                   373        2238000.0
16:04:23.380 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
16:04:23.380 INFO  BaseRecalibrator - Calculating quantized quality scores...
16:04:23.381 INFO  BaseRecalibrator - Writing recalibration report...
16:04:23.478 INFO  BaseRecalibrator - ...done!
16:04:23.478 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
16:04:23.478 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 4:04:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1568669696
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