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

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

tests
0

failures
0

ignored
43.210s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.067s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.064s passed
testBQSRFailWithoutDBSNP 0.062s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 4.672s 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 ')) 1.876s 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')) 0.496s 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')) 0.529s 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')) 0.493s 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')) 0.494s 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')) 0.770s 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')) 0.125s 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')) 5.673s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.122s 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')) 0.184s 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')) 6.238s 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')) 5.565s 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')) 5.569s 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')) 8.550s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.500s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.496s passed
testPlottingWorkflow 0.665s passed

Standard output

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[22:47:58] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[22:48:03] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[22:48:09] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[22:48:09] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[22:48:09] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[22:48:15] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[22:48:21] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[22:48:26] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[22:48:35] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[22:48:35] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[22:48:36] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[22:48:38] 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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[22:48:38] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[22:48:39] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[22:48:39] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[22:48:40] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[22:48:41] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[22:48:41] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[22:48:41] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[22:48:41] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[March 28, 2025 at 10:48:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:48:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
22:48:41.367 INFO  BaseRecalibrator - ------------------------------------------------------------
22:48:41.367 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
22:48:41.368 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
22:48:41.368 INFO  BaseRecalibrator - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:48:41.368 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:48:41.368 INFO  BaseRecalibrator - Start Date/Time: March 28, 2025 at 10:48:41 PM UTC
22:48:41.368 INFO  BaseRecalibrator - ------------------------------------------------------------
22:48:41.368 INFO  BaseRecalibrator - ------------------------------------------------------------
22:48:41.368 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:48:41.368 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:48:41.368 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:48:41.368 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:48:41.368 INFO  BaseRecalibrator - Deflater: IntelDeflater
22:48:41.368 INFO  BaseRecalibrator - Inflater: IntelInflater
22:48:41.368 INFO  BaseRecalibrator - GCS max retries/reopens: 20
22:48:41.368 INFO  BaseRecalibrator - Requester pays: disabled
22:48:41.368 INFO  BaseRecalibrator - Initializing engine
22:48:41.369 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
22:48:41.369 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
22:48:41.369 INFO  BaseRecalibrator - Done initializing engine
22:48:41.381 INFO  BaseRecalibrationEngine - The covariates being used here: 
22:48:41.381 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
22:48:41.381 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
22:48:41.381 INFO  BaseRecalibrationEngine - 	ContextCovariate
22:48:41.381 INFO  BaseRecalibrationEngine - 	CycleCovariate
22:48:41.382 INFO  ProgressMeter - Starting traversal
22:48:41.382 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:48:41.395 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
22:48:41.395 INFO  ProgressMeter -             unmapped              0.0                   373        1721538.5
22:48:41.395 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
22:48:41.396 INFO  BaseRecalibrator - Calculating quantized quality scores...
22:48:41.398 INFO  BaseRecalibrator - Writing recalibration report...
22:48:41.823 INFO  BaseRecalibrator - ...done!
22:48:41.823 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
22:48:41.823 INFO  BaseRecalibrator - Shutting down engine
[March 28, 2025 at 10:48:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
22:48:41.828 INFO  ApplyBQSR - ------------------------------------------------------------
22:48:41.828 INFO  ApplyBQSR - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
22:48:41.828 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
22:48:41.828 INFO  ApplyBQSR - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:48:41.828 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:48:41.828 INFO  ApplyBQSR - Start Date/Time: March 28, 2025 at 10:48:41 PM UTC
22:48:41.828 INFO  ApplyBQSR - ------------------------------------------------------------
22:48:41.828 INFO  ApplyBQSR - ------------------------------------------------------------
22:48:41.828 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:48:41.828 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:48:41.828 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:48:41.828 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:48:41.828 INFO  ApplyBQSR - Deflater: IntelDeflater
22:48:41.828 INFO  ApplyBQSR - Inflater: IntelInflater
22:48:41.828 INFO  ApplyBQSR - GCS max retries/reopens: 20
22:48:41.828 INFO  ApplyBQSR - Requester pays: disabled
22:48:41.828 INFO  ApplyBQSR - Initializing engine
22:48:41.828 INFO  ApplyBQSR - Done initializing engine
22:48:41.829 INFO  ProgressMeter - Starting traversal
22:48:41.829 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:48:41.879 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

22:48:41.879 INFO  ProgressMeter -             unmapped              0.0                   493         591600.0
22:48:41.879 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
22:48:41.929 INFO  ApplyBQSR - Shutting down engine
[March 28, 2025 at 10:48:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
22:48:41.934 INFO  BaseRecalibrator - ------------------------------------------------------------
22:48:41.934 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
22:48:41.934 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
22:48:41.934 INFO  BaseRecalibrator - Executing as runner@fv-az1690-153 on Linux v6.8.0-1021-azure amd64
22:48:41.934 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:48:41.934 INFO  BaseRecalibrator - Start Date/Time: March 28, 2025 at 10:48:41 PM UTC
22:48:41.934 INFO  BaseRecalibrator - ------------------------------------------------------------
22:48:41.934 INFO  BaseRecalibrator - ------------------------------------------------------------
22:48:41.934 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:48:41.934 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:48:41.934 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:48:41.934 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:48:41.934 INFO  BaseRecalibrator - Deflater: IntelDeflater
22:48:41.934 INFO  BaseRecalibrator - Inflater: IntelInflater
22:48:41.934 INFO  BaseRecalibrator - GCS max retries/reopens: 20
22:48:41.934 INFO  BaseRecalibrator - Requester pays: disabled
22:48:41.934 INFO  BaseRecalibrator - Initializing engine
22:48:41.935 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
22:48:41.935 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
22:48:41.936 INFO  BaseRecalibrator - Done initializing engine
22:48:41.942 INFO  BaseRecalibrationEngine - The covariates being used here: 
22:48:41.942 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
22:48:41.942 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
22:48:41.942 INFO  BaseRecalibrationEngine - 	ContextCovariate
22:48:41.942 INFO  BaseRecalibrationEngine - 	CycleCovariate
22:48:41.942 INFO  ProgressMeter - Starting traversal
22:48:41.942 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:48:41.952 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
22:48:41.953 INFO  ProgressMeter -             unmapped              0.0                   373        2034545.5
22:48:41.953 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
22:48:41.953 INFO  BaseRecalibrator - Calculating quantized quality scores...
22:48:41.954 INFO  BaseRecalibrator - Writing recalibration report...
22:48:42.020 INFO  BaseRecalibrator - ...done!
22:48:42.020 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
22:48:42.020 INFO  BaseRecalibrator - Shutting down engine
[March 28, 2025 at 10:48:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
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