[June 2, 2025 at 2:25:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:25:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
14:25:45.553 INFO BaseRecalibrator - ------------------------------------------------------------
14:25:45.553 INFO BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
14:25:45.553 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:25:45.553 INFO BaseRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:25:45.553 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:25:45.553 INFO BaseRecalibrator - Start Date/Time: June 2, 2025 at 2:25:45 PM UTC
14:25:45.553 INFO BaseRecalibrator - ------------------------------------------------------------
14:25:45.553 INFO BaseRecalibrator - ------------------------------------------------------------
14:25:45.553 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:25:45.553 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:25:45.553 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:25:45.553 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:25:45.553 INFO BaseRecalibrator - Deflater: IntelDeflater
14:25:45.553 INFO BaseRecalibrator - Inflater: IntelInflater
14:25:45.553 INFO BaseRecalibrator - GCS max retries/reopens: 20
14:25:45.553 INFO BaseRecalibrator - Requester pays: disabled
14:25:45.553 INFO BaseRecalibrator - Initializing engine
14:25:45.555 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
14:25:45.555 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
14:25:45.556 INFO BaseRecalibrator - Done initializing engine
14:25:45.567 INFO BaseRecalibrationEngine - The covariates being used here:
14:25:45.567 INFO BaseRecalibrationEngine - ReadGroupCovariate
14:25:45.567 INFO BaseRecalibrationEngine - QualityScoreCovariate
14:25:45.567 INFO BaseRecalibrationEngine - ContextCovariate
14:25:45.567 INFO BaseRecalibrationEngine - CycleCovariate
14:25:45.568 INFO ProgressMeter - Starting traversal
14:25:45.568 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:25:45.580 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
14:25:45.580 INFO ProgressMeter - unmapped 0.0 373 1865000.0
14:25:45.580 INFO ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
14:25:45.581 INFO BaseRecalibrator - Calculating quantized quality scores...
14:25:45.583 INFO BaseRecalibrator - Writing recalibration report...
14:25:45.996 INFO BaseRecalibrator - ...done!
14:25:45.996 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
14:25:45.996 INFO BaseRecalibrator - Shutting down engine
[June 2, 2025 at 2:25:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1663041536
14:25:46.000 INFO ApplyBQSR - ------------------------------------------------------------
14:25:46.001 INFO ApplyBQSR - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
14:25:46.001 INFO ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
14:25:46.001 INFO ApplyBQSR - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:25:46.001 INFO ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:25:46.001 INFO ApplyBQSR - Start Date/Time: June 2, 2025 at 2:25:45 PM UTC
14:25:46.001 INFO ApplyBQSR - ------------------------------------------------------------
14:25:46.001 INFO ApplyBQSR - ------------------------------------------------------------
14:25:46.001 INFO ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:25:46.001 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:25:46.001 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:25:46.001 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:25:46.001 INFO ApplyBQSR - Deflater: IntelDeflater
14:25:46.001 INFO ApplyBQSR - Inflater: IntelInflater
14:25:46.001 INFO ApplyBQSR - GCS max retries/reopens: 20
14:25:46.001 INFO ApplyBQSR - Requester pays: disabled
14:25:46.001 INFO ApplyBQSR - Initializing engine
14:25:46.001 INFO ApplyBQSR - Done initializing engine
14:25:46.002 INFO ProgressMeter - Starting traversal
14:25:46.002 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:25:46.049 INFO ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter
14:25:46.050 INFO ProgressMeter - unmapped 0.0 493 616250.0
14:25:46.050 INFO ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
14:25:46.100 INFO ApplyBQSR - Shutting down engine
[June 2, 2025 at 2:25:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
14:25:46.105 INFO BaseRecalibrator - ------------------------------------------------------------
14:25:46.105 INFO BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
14:25:46.105 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:25:46.105 INFO BaseRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
14:25:46.105 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:25:46.105 INFO BaseRecalibrator - Start Date/Time: June 2, 2025 at 2:25:46 PM UTC
14:25:46.105 INFO BaseRecalibrator - ------------------------------------------------------------
14:25:46.105 INFO BaseRecalibrator - ------------------------------------------------------------
14:25:46.105 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:25:46.105 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:25:46.105 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:25:46.105 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:25:46.105 INFO BaseRecalibrator - Deflater: IntelDeflater
14:25:46.105 INFO BaseRecalibrator - Inflater: IntelInflater
14:25:46.105 INFO BaseRecalibrator - GCS max retries/reopens: 20
14:25:46.105 INFO BaseRecalibrator - Requester pays: disabled
14:25:46.105 INFO BaseRecalibrator - Initializing engine
14:25:46.107 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
14:25:46.107 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
14:25:46.108 INFO BaseRecalibrator - Done initializing engine
14:25:46.114 INFO BaseRecalibrationEngine - The covariates being used here:
14:25:46.114 INFO BaseRecalibrationEngine - ReadGroupCovariate
14:25:46.114 INFO BaseRecalibrationEngine - QualityScoreCovariate
14:25:46.114 INFO BaseRecalibrationEngine - ContextCovariate
14:25:46.114 INFO BaseRecalibrationEngine - CycleCovariate
14:25:46.114 INFO ProgressMeter - Starting traversal
14:25:46.114 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
14:25:46.125 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
14:25:46.125 INFO ProgressMeter - unmapped 0.0 373 2034545.5
14:25:46.125 INFO ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
14:25:46.125 INFO BaseRecalibrator - Calculating quantized quality scores...
14:25:46.126 INFO BaseRecalibrator - Writing recalibration report...
14:25:46.195 INFO BaseRecalibrator - ...done!
14:25:46.195 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
14:25:46.195 INFO BaseRecalibrator - Shutting down engine
[June 2, 2025 at 2:25:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
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