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

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

tests
0

failures
0

ignored
1m2.00s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.092s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.090s passed
testBQSRFailWithoutDBSNP 0.088s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 6.741s 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 ')) 2.693s 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')) 0.698s 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')) 0.752s 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')) 0.697s 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')) 0.699s 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')) 1.075s 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')) 0.169s 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')) 8.114s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.191s 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')) 0.259s 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')) 8.998s 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')) 8.002s 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')) 8.017s 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')) 12.319s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.718s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.703s passed
testPlottingWorkflow 0.882s passed

Standard output

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[16:52:47] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[16:52:54] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[16:53:02] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[16:53:02] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[16:53:03] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[16:53:12] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[16:53:20] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[16:53:28] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[16:53:40] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[16:53:41] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[16:53:41] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[16:53:44] 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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[16:53:45] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[16:53:46] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[16:53:46] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[16:53:47] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[16:53:48] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[16:53:48] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[16:53:48] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[16:53:48] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[May 27, 2025 at 4:52:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:45 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:46 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:46 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1312817152
[May 27, 2025 at 4:53:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1312817152
16:53:48.955 INFO  BaseRecalibrator - ------------------------------------------------------------
16:53:48.955 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:53:48.955 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:53:48.955 INFO  BaseRecalibrator - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:53:48.955 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:53:48.955 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 4:53:48 PM GMT
16:53:48.955 INFO  BaseRecalibrator - ------------------------------------------------------------
16:53:48.955 INFO  BaseRecalibrator - ------------------------------------------------------------
16:53:48.955 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:53:48.955 INFO  BaseRecalibrator - Picard Version: 3.4.0
16:53:48.955 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
16:53:48.955 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:53:48.955 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:53:48.955 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:53:48.955 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:53:48.955 INFO  BaseRecalibrator - Deflater: IntelDeflater
16:53:48.955 INFO  BaseRecalibrator - Inflater: IntelInflater
16:53:48.955 INFO  BaseRecalibrator - GCS max retries/reopens: 20
16:53:48.955 INFO  BaseRecalibrator - Requester pays: disabled
16:53:48.955 INFO  BaseRecalibrator - Initializing engine
16:53:48.957 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
16:53:48.957 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
16:53:48.957 INFO  BaseRecalibrator - Done initializing engine
16:53:48.963 INFO  BaseRecalibrationEngine - The covariates being used here: 
16:53:48.963 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
16:53:48.963 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
16:53:48.963 INFO  BaseRecalibrationEngine - 	ContextCovariate
16:53:48.963 INFO  BaseRecalibrationEngine - 	CycleCovariate
16:53:48.964 INFO  ProgressMeter - Starting traversal
16:53:48.964 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:53:48.976 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
16:53:48.976 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
16:53:48.976 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
16:53:48.976 INFO  BaseRecalibrator - Calculating quantized quality scores...
16:53:48.978 INFO  BaseRecalibrator - Writing recalibration report...
16:53:49.561 INFO  BaseRecalibrator - ...done!
16:53:49.561 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
16:53:49.561 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 4:53:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1312817152
16:53:49.577 INFO  ApplyBQSR - ------------------------------------------------------------
16:53:49.577 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:53:49.577 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
16:53:49.577 INFO  ApplyBQSR - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:53:49.577 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:53:49.577 INFO  ApplyBQSR - Start Date/Time: May 27, 2025 at 4:53:49 PM GMT
16:53:49.577 INFO  ApplyBQSR - ------------------------------------------------------------
16:53:49.577 INFO  ApplyBQSR - ------------------------------------------------------------
16:53:49.577 INFO  ApplyBQSR - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:53:49.577 INFO  ApplyBQSR - Picard Version: 3.4.0
16:53:49.577 INFO  ApplyBQSR - Built for Spark Version: 3.5.0
16:53:49.577 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:53:49.577 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:53:49.577 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:53:49.577 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:53:49.577 INFO  ApplyBQSR - Deflater: IntelDeflater
16:53:49.577 INFO  ApplyBQSR - Inflater: IntelInflater
16:53:49.577 INFO  ApplyBQSR - GCS max retries/reopens: 20
16:53:49.577 INFO  ApplyBQSR - Requester pays: disabled
16:53:49.577 INFO  ApplyBQSR - Initializing engine
16:53:49.578 INFO  ApplyBQSR - Done initializing engine
16:53:49.578 INFO  ProgressMeter - Starting traversal
16:53:49.579 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:53:49.624 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

16:53:49.624 INFO  ProgressMeter -             unmapped              0.0                   493         657333.3
16:53:49.624 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
16:53:49.675 INFO  ApplyBQSR - Shutting down engine
[May 27, 2025 at 4:53:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1312817152
16:53:49.689 INFO  BaseRecalibrator - ------------------------------------------------------------
16:53:49.689 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-6-g113e5d7-SNAPSHOT
16:53:49.689 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:53:49.689 INFO  BaseRecalibrator - Executing as root@1c4c36ffc4f6 on Linux v6.11.0-1014-azure amd64
16:53:49.689 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:53:49.689 INFO  BaseRecalibrator - Start Date/Time: May 27, 2025 at 4:53:49 PM GMT
16:53:49.689 INFO  BaseRecalibrator - ------------------------------------------------------------
16:53:49.689 INFO  BaseRecalibrator - ------------------------------------------------------------
16:53:49.689 INFO  BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:53:49.689 INFO  BaseRecalibrator - Picard Version: 3.4.0
16:53:49.689 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0
16:53:49.689 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:53:49.689 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:53:49.689 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:53:49.689 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:53:49.689 INFO  BaseRecalibrator - Deflater: IntelDeflater
16:53:49.689 INFO  BaseRecalibrator - Inflater: IntelInflater
16:53:49.689 INFO  BaseRecalibrator - GCS max retries/reopens: 20
16:53:49.689 INFO  BaseRecalibrator - Requester pays: disabled
16:53:49.689 INFO  BaseRecalibrator - Initializing engine
16:53:49.691 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
16:53:49.692 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
16:53:49.692 INFO  BaseRecalibrator - Done initializing engine
16:53:49.700 INFO  BaseRecalibrationEngine - The covariates being used here: 
16:53:49.700 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
16:53:49.700 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
16:53:49.700 INFO  BaseRecalibrationEngine - 	ContextCovariate
16:53:49.700 INFO  BaseRecalibrationEngine - 	CycleCovariate
16:53:49.700 INFO  ProgressMeter - Starting traversal
16:53:49.700 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:53:49.712 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
16:53:49.712 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
16:53:49.712 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
16:53:49.712 INFO  BaseRecalibrator - Calculating quantized quality scores...
16:53:49.713 INFO  BaseRecalibrator - Writing recalibration report...
16:53:49.812 INFO  BaseRecalibrator - ...done!
16:53:49.812 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
16:53:49.812 INFO  BaseRecalibrator - Shutting down engine
[May 27, 2025 at 4:53:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1312817152
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