[May 19, 2025 at 4:04:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:04:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:04:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:04:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1402994688
[May 19, 2025 at 4:05:44 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1402994688
16:05:44.815 INFO BaseRecalibrator - ------------------------------------------------------------
16:05:44.815 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:05:44.815 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:05:44.815 INFO BaseRecalibrator - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:05:44.815 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:05:44.815 INFO BaseRecalibrator - Start Date/Time: May 19, 2025 at 4:05:44 PM GMT
16:05:44.815 INFO BaseRecalibrator - ------------------------------------------------------------
16:05:44.815 INFO BaseRecalibrator - ------------------------------------------------------------
16:05:44.815 INFO BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:05:44.815 INFO BaseRecalibrator - Picard Version: 3.4.0
16:05:44.815 INFO BaseRecalibrator - Built for Spark Version: 3.5.0
16:05:44.815 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:05:44.815 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:05:44.815 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:05:44.815 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:05:44.815 INFO BaseRecalibrator - Deflater: IntelDeflater
16:05:44.815 INFO BaseRecalibrator - Inflater: IntelInflater
16:05:44.815 INFO BaseRecalibrator - GCS max retries/reopens: 20
16:05:44.815 INFO BaseRecalibrator - Requester pays: disabled
16:05:44.815 INFO BaseRecalibrator - Initializing engine
16:05:44.817 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
16:05:44.818 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
16:05:44.818 INFO BaseRecalibrator - Done initializing engine
16:05:44.825 INFO BaseRecalibrationEngine - The covariates being used here:
16:05:44.825 INFO BaseRecalibrationEngine - ReadGroupCovariate
16:05:44.825 INFO BaseRecalibrationEngine - QualityScoreCovariate
16:05:44.825 INFO BaseRecalibrationEngine - ContextCovariate
16:05:44.825 INFO BaseRecalibrationEngine - CycleCovariate
16:05:44.825 INFO ProgressMeter - Starting traversal
16:05:44.825 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:05:44.838 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
16:05:44.838 INFO ProgressMeter - unmapped 0.0 373 1721538.5
16:05:44.838 INFO ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
16:05:44.838 INFO BaseRecalibrator - Calculating quantized quality scores...
16:05:44.840 INFO BaseRecalibrator - Writing recalibration report...
16:05:45.417 INFO BaseRecalibrator - ...done!
16:05:45.417 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
16:05:45.417 INFO BaseRecalibrator - Shutting down engine
[May 19, 2025 at 4:05:45 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1402994688
16:05:45.431 INFO ApplyBQSR - ------------------------------------------------------------
16:05:45.431 INFO ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:05:45.431 INFO ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
16:05:45.431 INFO ApplyBQSR - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:05:45.431 INFO ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:05:45.431 INFO ApplyBQSR - Start Date/Time: May 19, 2025 at 4:05:45 PM GMT
16:05:45.431 INFO ApplyBQSR - ------------------------------------------------------------
16:05:45.431 INFO ApplyBQSR - ------------------------------------------------------------
16:05:45.431 INFO ApplyBQSR - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:05:45.431 INFO ApplyBQSR - Picard Version: 3.4.0
16:05:45.431 INFO ApplyBQSR - Built for Spark Version: 3.5.0
16:05:45.432 INFO ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:05:45.432 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:05:45.432 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:05:45.432 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:05:45.432 INFO ApplyBQSR - Deflater: IntelDeflater
16:05:45.432 INFO ApplyBQSR - Inflater: IntelInflater
16:05:45.432 INFO ApplyBQSR - GCS max retries/reopens: 20
16:05:45.432 INFO ApplyBQSR - Requester pays: disabled
16:05:45.432 INFO ApplyBQSR - Initializing engine
16:05:45.432 INFO ApplyBQSR - Done initializing engine
16:05:45.433 INFO ProgressMeter - Starting traversal
16:05:45.433 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:05:45.484 INFO ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter
16:05:45.484 INFO ProgressMeter - unmapped 0.0 493 580000.0
16:05:45.484 INFO ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
16:05:45.535 INFO ApplyBQSR - Shutting down engine
[May 19, 2025 at 4:05:45 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1402994688
16:05:45.550 INFO BaseRecalibrator - ------------------------------------------------------------
16:05:45.550 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.2.0-4-ga6bd333-SNAPSHOT
16:05:45.550 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:05:45.550 INFO BaseRecalibrator - Executing as root@67ac59543751 on Linux v6.11.0-1014-azure amd64
16:05:45.550 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:05:45.550 INFO BaseRecalibrator - Start Date/Time: May 19, 2025 at 4:05:45 PM GMT
16:05:45.550 INFO BaseRecalibrator - ------------------------------------------------------------
16:05:45.550 INFO BaseRecalibrator - ------------------------------------------------------------
16:05:45.550 INFO BaseRecalibrator - HTSJDK Version: test_cram_wiring-SNAPSHOT
16:05:45.550 INFO BaseRecalibrator - Picard Version: 3.4.0
16:05:45.550 INFO BaseRecalibrator - Built for Spark Version: 3.5.0
16:05:45.550 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:05:45.550 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:05:45.550 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:05:45.550 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:05:45.550 INFO BaseRecalibrator - Deflater: IntelDeflater
16:05:45.550 INFO BaseRecalibrator - Inflater: IntelInflater
16:05:45.550 INFO BaseRecalibrator - GCS max retries/reopens: 20
16:05:45.550 INFO BaseRecalibrator - Requester pays: disabled
16:05:45.550 INFO BaseRecalibrator - Initializing engine
16:05:45.552 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
16:05:45.552 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
16:05:45.552 INFO BaseRecalibrator - Done initializing engine
16:05:45.559 INFO BaseRecalibrationEngine - The covariates being used here:
16:05:45.559 INFO BaseRecalibrationEngine - ReadGroupCovariate
16:05:45.559 INFO BaseRecalibrationEngine - QualityScoreCovariate
16:05:45.559 INFO BaseRecalibrationEngine - ContextCovariate
16:05:45.559 INFO BaseRecalibrationEngine - CycleCovariate
16:05:45.560 INFO ProgressMeter - Starting traversal
16:05:45.560 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:05:45.574 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
16:05:45.574 INFO ProgressMeter - unmapped 0.0 373 1598571.4
16:05:45.574 INFO ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
16:05:45.574 INFO BaseRecalibrator - Calculating quantized quality scores...
16:05:45.575 INFO BaseRecalibrator - Writing recalibration report...
16:05:45.672 INFO BaseRecalibrator - ...done!
16:05:45.672 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
16:05:45.672 INFO BaseRecalibrator - Shutting down engine
[May 19, 2025 at 4:05:45 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1402994688
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