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

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

tests
0

failures
0

ignored
43.991s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.074s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.072s passed
testBQSRFailWithoutDBSNP 0.069s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 4.624s 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 ')) 1.872s 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')) 0.538s 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')) 0.553s 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')) 0.540s 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')) 0.514s 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')) 0.811s 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')) 0.160s 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')) 5.674s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.160s 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')) 0.210s 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')) 6.356s 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')) 5.649s 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')) 5.772s 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')) 8.472s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.536s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.534s passed
testPlottingWorkflow 0.801s passed

Standard output

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[20:49:13] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[20:49:17] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[20:49:23] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[20:49:23] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[20:49:24] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[20:49:30] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[20:49:36] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[20:49:41] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[20:49:50] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[20:49:50] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[20:49:51] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[20:49:53] 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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[20:49:53] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[20:49:54] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[20:49:54] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[20:49:55] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[20:49:56] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[20:49:56] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[20:49:56] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[20:49:56] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[June 12, 2025 at 8:49:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
[June 12, 2025 at 8:49:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
20:49:56.553 INFO  BaseRecalibrator - ------------------------------------------------------------
20:49:56.553 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
20:49:56.553 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
20:49:56.553 INFO  BaseRecalibrator - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:49:56.553 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:49:56.553 INFO  BaseRecalibrator - Start Date/Time: June 12, 2025 at 8:49:56 PM UTC
20:49:56.553 INFO  BaseRecalibrator - ------------------------------------------------------------
20:49:56.553 INFO  BaseRecalibrator - ------------------------------------------------------------
20:49:56.553 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:49:56.553 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:49:56.553 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:49:56.553 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:49:56.553 INFO  BaseRecalibrator - Deflater: IntelDeflater
20:49:56.553 INFO  BaseRecalibrator - Inflater: IntelInflater
20:49:56.553 INFO  BaseRecalibrator - GCS max retries/reopens: 20
20:49:56.553 INFO  BaseRecalibrator - Requester pays: disabled
20:49:56.553 INFO  BaseRecalibrator - Initializing engine
20:49:56.554 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
20:49:56.555 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
20:49:56.555 INFO  BaseRecalibrator - Done initializing engine
20:49:56.585 INFO  Reflections - Reflections took 23 ms to scan 2 urls, producing 7 keys and 18 values 
20:49:56.586 INFO  BaseRecalibrationEngine - The covariates being used here: 
20:49:56.586 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
20:49:56.586 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
20:49:56.586 INFO  BaseRecalibrationEngine - 	ContextCovariate
20:49:56.586 INFO  BaseRecalibrationEngine - 	CycleCovariate
20:49:56.586 INFO  ProgressMeter - Starting traversal
20:49:56.586 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:49:56.598 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
20:49:56.598 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
20:49:56.598 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
20:49:56.599 INFO  BaseRecalibrator - Calculating quantized quality scores...
20:49:56.600 INFO  BaseRecalibrator - Writing recalibration report...
20:49:56.998 INFO  BaseRecalibrator - ...done!
20:49:56.998 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
20:49:56.999 INFO  BaseRecalibrator - Shutting down engine
[June 12, 2025 at 8:49:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1902116864
20:49:57.003 INFO  ApplyBQSR - ------------------------------------------------------------
20:49:57.003 INFO  ApplyBQSR - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
20:49:57.003 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
20:49:57.003 INFO  ApplyBQSR - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:49:57.003 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:49:57.003 INFO  ApplyBQSR - Start Date/Time: June 12, 2025 at 8:49:57 PM UTC
20:49:57.003 INFO  ApplyBQSR - ------------------------------------------------------------
20:49:57.003 INFO  ApplyBQSR - ------------------------------------------------------------
20:49:57.003 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:49:57.003 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:49:57.003 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:49:57.003 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:49:57.003 INFO  ApplyBQSR - Deflater: IntelDeflater
20:49:57.003 INFO  ApplyBQSR - Inflater: IntelInflater
20:49:57.003 INFO  ApplyBQSR - GCS max retries/reopens: 20
20:49:57.003 INFO  ApplyBQSR - Requester pays: disabled
20:49:57.003 INFO  ApplyBQSR - Initializing engine
20:49:57.004 INFO  ApplyBQSR - Done initializing engine
20:49:57.040 INFO  Reflections - Reflections took 23 ms to scan 2 urls, producing 7 keys and 18 values 
20:49:57.064 INFO  Reflections - Reflections took 23 ms to scan 2 urls, producing 7 keys and 18 values 
20:49:57.065 WARN  BQSRCovariateList - Covariate ReadGroupCovariate is a required covariate that is always on. Ignoring explicit request for it.
20:49:57.065 WARN  BQSRCovariateList - Covariate QualityScoreCovariate is a required covariate that is always on. Ignoring explicit request for it.
20:49:57.065 WARN  BQSRCovariateList - Covariate ContextCovariate is a standard covariate that is always on when not running with --no-standard-covariates. Ignoring explicit request for it.
20:49:57.065 WARN  BQSRCovariateList - Covariate CycleCovariate is a standard covariate that is always on when not running with --no-standard-covariates. Ignoring explicit request for it.
20:49:57.074 INFO  ApplyBQSR - Loaded covariates ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate from recalibration table /tmp/local13085480587404488327/gatk4.pre.cols8176656714873256721.table
20:49:57.074 INFO  ProgressMeter - Starting traversal
20:49:57.074 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:49:57.114 INFO  Reflections - Reflections took 24 ms to scan 2 urls, producing 7 keys and 18 values 
20:49:57.138 INFO  Reflections - Reflections took 24 ms to scan 2 urls, producing 7 keys and 18 values 
20:49:57.138 WARN  BQSRCovariateList - Covariate ReadGroupCovariate is a required covariate that is always on. Ignoring explicit request for it.
20:49:57.138 WARN  BQSRCovariateList - Covariate QualityScoreCovariate is a required covariate that is always on. Ignoring explicit request for it.
20:49:57.138 WARN  BQSRCovariateList - Covariate ContextCovariate is a standard covariate that is always on when not running with --no-standard-covariates. Ignoring explicit request for it.
20:49:57.138 WARN  BQSRCovariateList - Covariate CycleCovariate is a standard covariate that is always on when not running with --no-standard-covariates. Ignoring explicit request for it.
20:49:57.172 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

20:49:57.172 INFO  ProgressMeter -             unmapped              0.0                   493         301836.7
20:49:57.172 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
20:49:57.223 INFO  ApplyBQSR - Shutting down engine
[June 12, 2025 at 8:49:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
20:49:57.228 INFO  BaseRecalibrator - ------------------------------------------------------------
20:49:57.228 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
20:49:57.228 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
20:49:57.228 INFO  BaseRecalibrator - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:49:57.228 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:49:57.228 INFO  BaseRecalibrator - Start Date/Time: June 12, 2025 at 8:49:57 PM UTC
20:49:57.228 INFO  BaseRecalibrator - ------------------------------------------------------------
20:49:57.229 INFO  BaseRecalibrator - ------------------------------------------------------------
20:49:57.229 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:49:57.229 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:49:57.229 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:49:57.229 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:49:57.229 INFO  BaseRecalibrator - Deflater: IntelDeflater
20:49:57.229 INFO  BaseRecalibrator - Inflater: IntelInflater
20:49:57.229 INFO  BaseRecalibrator - GCS max retries/reopens: 20
20:49:57.229 INFO  BaseRecalibrator - Requester pays: disabled
20:49:57.229 INFO  BaseRecalibrator - Initializing engine
20:49:57.230 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
20:49:57.231 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
20:49:57.231 INFO  BaseRecalibrator - Done initializing engine
20:49:57.261 INFO  Reflections - Reflections took 24 ms to scan 2 urls, producing 7 keys and 18 values 
20:49:57.261 INFO  BaseRecalibrationEngine - The covariates being used here: 
20:49:57.261 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
20:49:57.261 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
20:49:57.261 INFO  BaseRecalibrationEngine - 	ContextCovariate
20:49:57.261 INFO  BaseRecalibrationEngine - 	CycleCovariate
20:49:57.262 INFO  ProgressMeter - Starting traversal
20:49:57.262 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:49:57.272 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
20:49:57.272 INFO  ProgressMeter -             unmapped              0.0                   373        2238000.0
20:49:57.272 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
20:49:57.272 INFO  BaseRecalibrator - Calculating quantized quality scores...
20:49:57.273 INFO  BaseRecalibrator - Writing recalibration report...
20:49:57.340 INFO  BaseRecalibrator - ...done!
20:49:57.340 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
20:49:57.340 INFO  BaseRecalibrator - Shutting down engine
[June 12, 2025 at 8:49:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1902116864
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