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

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

tests
0

failures
0

ignored
1m1.66s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.086s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.085s passed
testBQSRFailWithoutDBSNP 0.080s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 6.675s passed
testBQSR[10](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.4379150-4379157.bam', args='-indels --enable-baq ')) 2.686s 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')) 0.685s 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')) 0.778s 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')) 0.690s 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')) 0.689s passed
testBQSR[15](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --mismatches-context-size 4')) 1.064s 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')) 0.167s passed
testBQSR[1](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq')) 8.222s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.168s 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')) 0.255s passed
testBQSR[4](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --indels-context-size 4')) 8.865s passed
testBQSR[5](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --low-quality-tail 5')) 7.944s passed
testBQSR[6](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --quantizing-levels 6')) 7.959s passed
testBQSR[7](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --mismatches-context-size 4')) 12.287s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.703s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.700s passed
testPlottingWorkflow 0.875s passed

Standard output

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[19:16:50] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[19:16:57] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[19:17:05] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[19:17:05] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[19:17:06] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[19:17:15] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[19:17:23] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[19:17:30] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[19:17:43] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[19:17:43] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[19:17:44] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[19:17:47] 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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[19:17:48] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[19:17:48] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[19:17:49] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[19:17:50] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[19:17:51] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[19:17:51] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[19:17:51] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[19:17:51] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[May 19, 2025 at 7:16:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1306525696
[May 19, 2025 at 7:17:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1306525696
19:17:51.688 INFO  BaseRecalibrator - ------------------------------------------------------------
19:17:51.688 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:17:51.688 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:17:51.688 INFO  BaseRecalibrator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:17:51.688 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:17:51.688 INFO  BaseRecalibrator - Start Date/Time: May 19, 2025 at 7:17:51 PM GMT
19:17:51.688 INFO  BaseRecalibrator - ------------------------------------------------------------
19:17:51.688 INFO  BaseRecalibrator - ------------------------------------------------------------
19:17:51.688 INFO  BaseRecalibrator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:17:51.688 INFO  BaseRecalibrator - Picard Version: 3.4.0
19:17:51.688 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
19:17:51.688 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:17:51.688 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:17:51.689 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:17:51.689 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:17:51.689 INFO  BaseRecalibrator - Deflater: IntelDeflater
19:17:51.689 INFO  BaseRecalibrator - Inflater: IntelInflater
19:17:51.689 INFO  BaseRecalibrator - GCS max retries/reopens: 20
19:17:51.689 INFO  BaseRecalibrator - Requester pays: disabled
19:17:51.689 INFO  BaseRecalibrator - Initializing engine
19:17:51.690 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf
19:17:51.691 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
19:17:51.691 INFO  BaseRecalibrator - Done initializing engine
19:17:51.697 INFO  BaseRecalibrationEngine - The covariates being used here: 
19:17:51.697 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
19:17:51.697 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
19:17:51.697 INFO  BaseRecalibrationEngine - 	ContextCovariate
19:17:51.697 INFO  BaseRecalibrationEngine - 	CycleCovariate
19:17:51.697 INFO  ProgressMeter - Starting traversal
19:17:51.697 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:17:51.709 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
19:17:51.709 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
19:17:51.709 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
19:17:51.710 INFO  BaseRecalibrator - Calculating quantized quality scores...
19:17:51.712 INFO  BaseRecalibrator - Writing recalibration report...
19:17:52.294 INFO  BaseRecalibrator - ...done!
19:17:52.294 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
19:17:52.294 INFO  BaseRecalibrator - Shutting down engine
[May 19, 2025 at 7:17:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1306525696
19:17:52.308 INFO  ApplyBQSR - ------------------------------------------------------------
19:17:52.308 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:17:52.308 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
19:17:52.308 INFO  ApplyBQSR - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:17:52.308 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:17:52.308 INFO  ApplyBQSR - Start Date/Time: May 19, 2025 at 7:17:52 PM GMT
19:17:52.308 INFO  ApplyBQSR - ------------------------------------------------------------
19:17:52.308 INFO  ApplyBQSR - ------------------------------------------------------------
19:17:52.308 INFO  ApplyBQSR - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:17:52.308 INFO  ApplyBQSR - Picard Version: 3.4.0
19:17:52.308 INFO  ApplyBQSR - Built for Spark Version: 3.5.0
19:17:52.308 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:17:52.308 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:17:52.308 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:17:52.308 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:17:52.308 INFO  ApplyBQSR - Deflater: IntelDeflater
19:17:52.308 INFO  ApplyBQSR - Inflater: IntelInflater
19:17:52.308 INFO  ApplyBQSR - GCS max retries/reopens: 20
19:17:52.308 INFO  ApplyBQSR - Requester pays: disabled
19:17:52.308 INFO  ApplyBQSR - Initializing engine
19:17:52.308 INFO  ApplyBQSR - Done initializing engine
19:17:52.309 INFO  ProgressMeter - Starting traversal
19:17:52.309 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:17:52.360 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

19:17:52.360 INFO  ProgressMeter -             unmapped              0.0                   493         580000.0
19:17:52.360 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
19:17:52.410 INFO  ApplyBQSR - Shutting down engine
[May 19, 2025 at 7:17:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1306525696
19:17:52.424 INFO  BaseRecalibrator - ------------------------------------------------------------
19:17:52.424 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-5-g0192957-SNAPSHOT
19:17:52.424 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:17:52.424 INFO  BaseRecalibrator - Executing as root@39b899212c20 on Linux v6.11.0-1014-azure amd64
19:17:52.424 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
19:17:52.424 INFO  BaseRecalibrator - Start Date/Time: May 19, 2025 at 7:17:52 PM GMT
19:17:52.424 INFO  BaseRecalibrator - ------------------------------------------------------------
19:17:52.424 INFO  BaseRecalibrator - ------------------------------------------------------------
19:17:52.424 INFO  BaseRecalibrator - HTSJDK Version: 4.2.0-7-gb6a1842-SNAPSHOT
19:17:52.424 INFO  BaseRecalibrator - Picard Version: 3.4.0
19:17:52.424 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
19:17:52.424 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:17:52.424 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:17:52.424 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:17:52.424 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:17:52.424 INFO  BaseRecalibrator - Deflater: IntelDeflater
19:17:52.424 INFO  BaseRecalibrator - Inflater: IntelInflater
19:17:52.424 INFO  BaseRecalibrator - GCS max retries/reopens: 20
19:17:52.425 INFO  BaseRecalibrator - Requester pays: disabled
19:17:52.425 INFO  BaseRecalibrator - Initializing engine
19:17:52.426 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf
19:17:52.426 WARN  IndexUtils - Feature file "file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
19:17:52.427 INFO  BaseRecalibrator - Done initializing engine
19:17:52.433 INFO  BaseRecalibrationEngine - The covariates being used here: 
19:17:52.433 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
19:17:52.433 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
19:17:52.433 INFO  BaseRecalibrationEngine - 	ContextCovariate
19:17:52.433 INFO  BaseRecalibrationEngine - 	CycleCovariate
19:17:52.433 INFO  ProgressMeter - Starting traversal
19:17:52.433 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
19:17:52.444 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
19:17:52.444 INFO  ProgressMeter -             unmapped              0.0                   373        2034545.5
19:17:52.444 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
19:17:52.444 INFO  BaseRecalibrator - Calculating quantized quality scores...
19:17:52.445 INFO  BaseRecalibrator - Writing recalibration report...
19:17:52.541 INFO  BaseRecalibrator - ...done!
19:17:52.541 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
19:17:52.541 INFO  BaseRecalibrator - Shutting down engine
[May 19, 2025 at 7:17:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1306525696
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