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

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

tests
0

failures
0

ignored
43.926s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.071s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.068s passed
testBQSRFailWithoutDBSNP 0.066s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 4.760s 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 ')) 1.893s 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')) 0.503s 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')) 0.537s 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')) 0.506s 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')) 0.496s 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')) 0.761s 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')) 0.134s 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')) 5.792s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.143s 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')) 0.186s 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')) 6.386s 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')) 5.617s 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')) 5.603s 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')) 8.731s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.526s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.504s passed
testPlottingWorkflow 0.643s passed

Standard output

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[15:47:56] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[15:48:01] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[15:48:06] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[15:48:07] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[15:48:07] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[15:48:13] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[15:48:19] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[15:48:24] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[15:48:33] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[15:48:34] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[15:48:34] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[15:48:36] 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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[15:48:37] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[15:48:37] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[15:48:38] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[15:48:38] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[15:48:39] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[15:48:39] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[15:48:39] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[15:48:39] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[May 19, 2025 at 3:48:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:48:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
15:48:39.731 INFO  BaseRecalibrator - ------------------------------------------------------------
15:48:39.731 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
15:48:39.731 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:48:39.731 INFO  BaseRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:48:39.731 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:48:39.731 INFO  BaseRecalibrator - Start Date/Time: May 19, 2025 at 3:48:39 PM UTC
15:48:39.731 INFO  BaseRecalibrator - ------------------------------------------------------------
15:48:39.731 INFO  BaseRecalibrator - ------------------------------------------------------------
15:48:39.731 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:48:39.731 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:48:39.731 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:48:39.731 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:48:39.731 INFO  BaseRecalibrator - Deflater: IntelDeflater
15:48:39.731 INFO  BaseRecalibrator - Inflater: IntelInflater
15:48:39.731 INFO  BaseRecalibrator - GCS max retries/reopens: 20
15:48:39.731 INFO  BaseRecalibrator - Requester pays: disabled
15:48:39.731 INFO  BaseRecalibrator - Initializing engine
15:48:39.733 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
15:48:39.733 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
15:48:39.733 INFO  BaseRecalibrator - Done initializing engine
15:48:39.739 INFO  BaseRecalibrationEngine - The covariates being used here: 
15:48:39.740 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
15:48:39.740 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
15:48:39.740 INFO  BaseRecalibrationEngine - 	ContextCovariate
15:48:39.740 INFO  BaseRecalibrationEngine - 	CycleCovariate
15:48:39.740 INFO  ProgressMeter - Starting traversal
15:48:39.740 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
15:48:39.752 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
15:48:39.752 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
15:48:39.752 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
15:48:39.752 INFO  BaseRecalibrator - Calculating quantized quality scores...
15:48:39.754 INFO  BaseRecalibrator - Writing recalibration report...
15:48:40.160 INFO  BaseRecalibrator - ...done!
15:48:40.160 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
15:48:40.160 INFO  BaseRecalibrator - Shutting down engine
[May 19, 2025 at 3:48:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1337982976
15:48:40.165 INFO  ApplyBQSR - ------------------------------------------------------------
15:48:40.165 INFO  ApplyBQSR - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
15:48:40.165 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
15:48:40.165 INFO  ApplyBQSR - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:48:40.165 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:48:40.165 INFO  ApplyBQSR - Start Date/Time: May 19, 2025 at 3:48:40 PM UTC
15:48:40.165 INFO  ApplyBQSR - ------------------------------------------------------------
15:48:40.165 INFO  ApplyBQSR - ------------------------------------------------------------
15:48:40.165 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:48:40.165 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:48:40.165 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:48:40.165 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:48:40.165 INFO  ApplyBQSR - Deflater: IntelDeflater
15:48:40.165 INFO  ApplyBQSR - Inflater: IntelInflater
15:48:40.165 INFO  ApplyBQSR - GCS max retries/reopens: 20
15:48:40.165 INFO  ApplyBQSR - Requester pays: disabled
15:48:40.165 INFO  ApplyBQSR - Initializing engine
15:48:40.166 INFO  ApplyBQSR - Done initializing engine
15:48:40.166 INFO  ProgressMeter - Starting traversal
15:48:40.166 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
15:48:40.216 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

15:48:40.216 INFO  ProgressMeter -             unmapped              0.0                   493         591600.0
15:48:40.216 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
15:48:40.266 INFO  ApplyBQSR - Shutting down engine
[May 19, 2025 at 3:48:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
15:48:40.271 INFO  BaseRecalibrator - ------------------------------------------------------------
15:48:40.271 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
15:48:40.271 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:48:40.271 INFO  BaseRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:48:40.271 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:48:40.271 INFO  BaseRecalibrator - Start Date/Time: May 19, 2025 at 3:48:40 PM UTC
15:48:40.271 INFO  BaseRecalibrator - ------------------------------------------------------------
15:48:40.271 INFO  BaseRecalibrator - ------------------------------------------------------------
15:48:40.271 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:48:40.271 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:48:40.272 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:48:40.272 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:48:40.272 INFO  BaseRecalibrator - Deflater: IntelDeflater
15:48:40.272 INFO  BaseRecalibrator - Inflater: IntelInflater
15:48:40.272 INFO  BaseRecalibrator - GCS max retries/reopens: 20
15:48:40.272 INFO  BaseRecalibrator - Requester pays: disabled
15:48:40.272 INFO  BaseRecalibrator - Initializing engine
15:48:40.273 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
15:48:40.274 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
15:48:40.274 INFO  BaseRecalibrator - Done initializing engine
15:48:40.280 INFO  BaseRecalibrationEngine - The covariates being used here: 
15:48:40.280 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
15:48:40.280 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
15:48:40.280 INFO  BaseRecalibrationEngine - 	ContextCovariate
15:48:40.280 INFO  BaseRecalibrationEngine - 	CycleCovariate
15:48:40.280 INFO  ProgressMeter - Starting traversal
15:48:40.280 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
15:48:40.291 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
15:48:40.291 INFO  ProgressMeter -             unmapped              0.0                   373        2034545.5
15:48:40.291 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
15:48:40.291 INFO  BaseRecalibrator - Calculating quantized quality scores...
15:48:40.292 INFO  BaseRecalibrator - Writing recalibration report...
15:48:40.360 INFO  BaseRecalibrator - ...done!
15:48:40.360 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
15:48:40.360 INFO  BaseRecalibrator - Shutting down engine
[May 19, 2025 at 3:48:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
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