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

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

tests
0

failures
0

ignored
43.832s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.072s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.070s passed
testBQSRFailWithoutDBSNP 0.067s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 4.725s 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 ')) 1.897s 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')) 0.500s 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')) 0.546s 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')) 0.505s 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')) 0.498s 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')) 0.765s 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')) 0.128s 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')) 5.778s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.131s 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')) 0.191s 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')) 6.397s 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')) 5.614s 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')) 5.618s 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')) 8.678s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.510s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.493s passed
testPlottingWorkflow 0.649s passed

Standard output

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[13:52:56] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[13:53:01] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[13:53:07] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[13:53:07] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[13:53:07] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[13:53:14] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[13:53:19] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[13:53:25] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[13:53:34] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[13:53:34] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[13:53:35] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[13:53:37] 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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[13:53:37] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[13:53:38] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[13:53:38] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[13:53:39] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[13:53:39] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[13:53:39] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[13:53:40] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[13:53:40] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[May 27, 2025 at 1:53:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:53:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
13:53:40.180 INFO  BaseRecalibrator - ------------------------------------------------------------
13:53:40.180 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
13:53:40.180 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:53:40.180 INFO  BaseRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:53:40.180 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:53:40.180 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 1:53:40 PM UTC
13:53:40.180 INFO  BaseRecalibrator - ------------------------------------------------------------
13:53:40.180 INFO  BaseRecalibrator - ------------------------------------------------------------
13:53:40.180 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:53:40.180 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:53:40.180 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:53:40.180 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:53:40.180 INFO  BaseRecalibrator - Deflater: IntelDeflater
13:53:40.180 INFO  BaseRecalibrator - Inflater: IntelInflater
13:53:40.181 INFO  BaseRecalibrator - GCS max retries/reopens: 20
13:53:40.181 INFO  BaseRecalibrator - Requester pays: disabled
13:53:40.181 INFO  BaseRecalibrator - Initializing engine
13:53:40.182 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf
13:53:40.182 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/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
13:53:40.183 INFO  BaseRecalibrator - Done initializing engine
13:53:40.199 INFO  BaseRecalibrationEngine - The covariates being used here: 
13:53:40.199 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
13:53:40.199 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
13:53:40.199 INFO  BaseRecalibrationEngine - 	ContextCovariate
13:53:40.199 INFO  BaseRecalibrationEngine - 	CycleCovariate
13:53:40.199 INFO  ProgressMeter - Starting traversal
13:53:40.199 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
13:53:40.211 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
13:53:40.211 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
13:53:40.211 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
13:53:40.212 INFO  BaseRecalibrator - Calculating quantized quality scores...
13:53:40.214 INFO  BaseRecalibrator - Writing recalibration report...
13:53:40.618 INFO  BaseRecalibrator - ...done!
13:53:40.618 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
13:53:40.618 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 1:53:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2032140288
13:53:40.623 INFO  ApplyBQSR - ------------------------------------------------------------
13:53:40.623 INFO  ApplyBQSR - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
13:53:40.623 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
13:53:40.623 INFO  ApplyBQSR - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:53:40.623 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:53:40.623 INFO  ApplyBQSR - Start Date/Time: May 27, 2025 at 1:53:40 PM UTC
13:53:40.623 INFO  ApplyBQSR - ------------------------------------------------------------
13:53:40.623 INFO  ApplyBQSR - ------------------------------------------------------------
13:53:40.623 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:53:40.623 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:53:40.623 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:53:40.623 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:53:40.623 INFO  ApplyBQSR - Deflater: IntelDeflater
13:53:40.623 INFO  ApplyBQSR - Inflater: IntelInflater
13:53:40.623 INFO  ApplyBQSR - GCS max retries/reopens: 20
13:53:40.623 INFO  ApplyBQSR - Requester pays: disabled
13:53:40.623 INFO  ApplyBQSR - Initializing engine
13:53:40.623 INFO  ApplyBQSR - Done initializing engine
13:53:40.624 INFO  ProgressMeter - Starting traversal
13:53:40.624 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
13:53:40.670 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

13:53:40.670 INFO  ProgressMeter -             unmapped              0.0                   493         643043.5
13:53:40.670 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
13:53:40.721 INFO  ApplyBQSR - Shutting down engine
[May 27, 2025 at 1:53:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
13:53:40.725 INFO  BaseRecalibrator - ------------------------------------------------------------
13:53:40.725 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
13:53:40.725 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:53:40.725 INFO  BaseRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
13:53:40.725 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
13:53:40.725 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 1:53:40 PM UTC
13:53:40.725 INFO  BaseRecalibrator - ------------------------------------------------------------
13:53:40.725 INFO  BaseRecalibrator - ------------------------------------------------------------
13:53:40.726 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:53:40.726 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:53:40.726 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:53:40.726 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:53:40.726 INFO  BaseRecalibrator - Deflater: IntelDeflater
13:53:40.726 INFO  BaseRecalibrator - Inflater: IntelInflater
13:53:40.726 INFO  BaseRecalibrator - GCS max retries/reopens: 20
13:53:40.726 INFO  BaseRecalibrator - Requester pays: disabled
13:53:40.726 INFO  BaseRecalibrator - Initializing engine
13:53:40.727 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf
13:53:40.727 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/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
13:53:40.728 INFO  BaseRecalibrator - Done initializing engine
13:53:40.733 INFO  BaseRecalibrationEngine - The covariates being used here: 
13:53:40.733 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
13:53:40.733 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
13:53:40.733 INFO  BaseRecalibrationEngine - 	ContextCovariate
13:53:40.734 INFO  BaseRecalibrationEngine - 	CycleCovariate
13:53:40.734 INFO  ProgressMeter - Starting traversal
13:53:40.734 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
13:53:40.744 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
13:53:40.744 INFO  ProgressMeter -             unmapped              0.0                   373        2238000.0
13:53:40.744 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
13:53:40.745 INFO  BaseRecalibrator - Calculating quantized quality scores...
13:53:40.746 INFO  BaseRecalibrator - Writing recalibration report...
13:53:40.813 INFO  BaseRecalibrator - ...done!
13:53:40.813 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
13:53:40.813 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 1:53:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
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