[May 27, 2025 at 6:24:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=799014912
18:24:23.077 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:23.078 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:23.078 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:23.078 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:23.078 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:23.078 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:23 PM UTC
18:24:23.079 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:23.079 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:23.079 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:23.079 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:23.079 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:23.079 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:23.079 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:23.079 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:23.079 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:23.080 INFO VariantRecalibrator - Requester pays: disabled
18:24:23.080 INFO VariantRecalibrator - Initializing engine
18:24:23.082 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/chr1snippet.doctoredMQ.sites_only.vcf.gz
18:24:23.099 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/chr1snippet.doctoredMQ.sites_only.vcf.gz
18:24:23.156 INFO IntervalArgumentCollection - Processing 10000000 bp from intervals
18:24:23.178 INFO VariantRecalibrator - Done initializing engine
18:24:23.179 INFO TrainingSet - Found same track: Known = false Training = true Truth = true Prior = Q15.0
18:24:23.207 INFO ProgressMeter - Starting traversal
18:24:23.208 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:23.294 INFO ProgressMeter - chr1:6212018 0.0 2791 1947209.3
18:24:23.295 INFO ProgressMeter - Traversal complete. Processed 2791 total variants in 0.0 minutes.
18:24:23.296 INFO VariantDataManager - AS_QD: mean = 20.88 standard deviation = 8.12
18:24:23.297 INFO VariantDataManager - AS_ReadPosRankSum: mean = -0.05 standard deviation = 0.74
18:24:23.298 INFO VariantDataManager - AS_MQ: mean = 59.82 standard deviation = 2.48
18:24:23.298 INFO VariantDataManager - AS_SOR: mean = 0.86 standard deviation = 0.67
18:24:23.302 INFO VariantDataManager - Annotation order is: [AS_QD, AS_ReadPosRankSum, AS_MQ, AS_SOR]
18:24:23.302 INFO VariantDataManager - Training with 2774 variants after standard deviation thresholding.
18:24:23.302 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:23.332 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:23.349 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.16919
18:24:23.366 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.14268
18:24:23.383 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.19617
18:24:23.400 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.09047
18:24:23.417 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.05235
18:24:23.433 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04028
18:24:23.450 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02103
18:24:23.476 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01461
18:24:23.491 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.01136
18:24:23.507 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00583
18:24:23.527 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00291
18:24:23.536 INFO VariantRecalibratorEngine - Convergence after 58 iterations!
18:24:23.538 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
18:24:23.547 INFO VariantDataManager - Selected worst 0 scoring variants --> variants with LOD <= -5.5000.
18:24:23.554 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=799014912
18:24:23.559 INFO gatk - Initializing VQSR tests/resetting random number generator
18:24:23.575 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:23.575 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:23.575 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:23.575 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:23.575 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:23.575 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:23 PM UTC
18:24:23.575 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:23.576 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:23.576 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:23.576 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:23.576 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:23.576 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:23.576 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:23.576 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:23.576 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:23.577 INFO VariantRecalibrator - Requester pays: disabled
18:24:23.577 INFO VariantRecalibrator - Initializing engine
18:24:23.578 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/dbsnp_132_b37.leftAligned.20.1M-10M.vcf
18:24:23.581 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/sites_r27_nr.b37_fwd.20.1M-10M.vcf
18:24:23.584 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf
18:24:23.586 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf
18:24:23.589 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
18:24:23.590 INFO VariantRecalibrator - Done initializing engine
18:24:23.592 WARN VariantDataManager - Ignoring duplicate annotations for recalibration [HRun]
18:24:23.592 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
18:24:23.592 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
18:24:23.593 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
18:24:23.595 INFO ProgressMeter - Starting traversal
18:24:23.595 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:24.630 INFO ProgressMeter - 20:9944766 0.0 131821 7649187.6
18:24:24.630 INFO ProgressMeter - Traversal complete. Processed 131821 total variants in 0.0 minutes.
18:24:24.634 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
18:24:24.638 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
18:24:24.640 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
18:24:24.660 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
18:24:24.662 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
18:24:24.662 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:24.900 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:25.003 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.42302
18:24:25.108 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24203
18:24:25.215 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15214
18:24:25.324 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.22858
18:24:25.434 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07799
18:24:25.541 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04227
18:24:25.649 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00976
18:24:25.738 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03859
18:24:25.826 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.18953
18:24:25.915 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01049
18:24:25.986 INFO VariantRecalibratorEngine - Convergence after 54 iterations!
18:24:25.992 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
18:24:26.060 INFO VariantDataManager - Selected worst 474 scoring variants --> variants with LOD <= -5.0000.
18:24:26.060 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:26.062 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:26.062 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
18:24:26.064 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
18:24:26.239 INFO TrancheManager - Finding 4 tranches for 131821 variants
18:24:26.270 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
18:24:26.275 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
18:24:26.275 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-240.7209 known=(59500 @ 2.2991) novel=(72321 @ 2.2239) truthSites(18665 accessible, 18665 called), name=anonymous]
18:24:26.275 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
18:24:26.280 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 747; running score is 0.001
18:24:26.280 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-3.1318 known=(59151 @ 2.3066) novel=(71923 @ 2.2295) truthSites(18665 accessible, 18646 called), name=anonymous]
18:24:26.280 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
18:24:26.285 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 5604; running score is 0.010
18:24:26.285 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=2.2535 known=(57628 @ 2.3617) novel=(68589 @ 2.2769) truthSites(18665 accessible, 18478 called), name=anonymous]
18:24:26.285 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
18:24:26.289 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 63492; running score is 0.100
18:24:26.290 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=7.6928 known=(45852 @ 2.4660) novel=(22477 @ 2.4146) truthSites(18665 accessible, 16798 called), name=anonymous]
18:24:26.290 INFO VariantRecalibrator - Writing out recalibration table...
18:24:26.711 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=989855744
18:24:26.750 INFO gatk - Initializing VQSR tests/resetting random number generator
18:24:26.769 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:26.769 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:26.769 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:26.769 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:26.769 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:26.770 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:26 PM UTC
18:24:26.770 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:26.770 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:26.770 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:26.770 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:26.770 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:26.771 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:26.771 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:26.771 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:26.771 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:26.771 INFO VariantRecalibrator - Requester pays: disabled
18:24:26.771 INFO VariantRecalibrator - Initializing engine
18:24:26.772 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/dbsnp_132_b37.leftAligned.20.1M-10M.vcf
18:24:26.776 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/sites_r27_nr.b37_fwd.20.1M-10M.vcf
18:24:26.778 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf
18:24:26.784 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf
18:24:26.787 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
18:24:26.788 INFO VariantRecalibrator - Done initializing engine
18:24:26.788 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
18:24:26.789 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
18:24:26.789 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
18:24:26.790 INFO ProgressMeter - Starting traversal
18:24:26.791 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:27.737 INFO ProgressMeter - 20:9944766 0.0 131821 8360740.0
18:24:27.737 INFO ProgressMeter - Traversal complete. Processed 131821 total variants in 0.0 minutes.
18:24:27.740 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
18:24:27.743 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
18:24:27.746 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
18:24:27.770 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
18:24:27.771 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
18:24:27.772 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:28.011 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:28.114 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.42302
18:24:28.224 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24203
18:24:28.311 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15214
18:24:28.398 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.22858
18:24:28.486 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07799
18:24:28.573 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04227
18:24:28.661 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00976
18:24:28.750 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03859
18:24:28.840 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.18953
18:24:28.929 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01049
18:24:29.009 INFO VariantRecalibratorEngine - Convergence after 54 iterations!
18:24:29.015 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
18:24:29.087 INFO VariantDataManager - Selected worst 474 scoring variants --> variants with LOD <= -5.0000.
18:24:29.087 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:29.088 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:29.089 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
18:24:29.090 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
18:24:29.272 INFO TrancheManager - Finding 4 tranches for 131821 variants
18:24:29.303 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
18:24:29.307 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
18:24:29.308 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-240.7209 known=(59500 @ 2.2991) novel=(72321 @ 2.2239) truthSites(18665 accessible, 18665 called), name=anonymous]
18:24:29.308 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
18:24:29.312 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 747; running score is 0.001
18:24:29.312 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-3.1318 known=(59151 @ 2.3066) novel=(71923 @ 2.2295) truthSites(18665 accessible, 18646 called), name=anonymous]
18:24:29.312 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
18:24:29.316 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 5604; running score is 0.010
18:24:29.317 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=2.2535 known=(57628 @ 2.3617) novel=(68589 @ 2.2769) truthSites(18665 accessible, 18478 called), name=anonymous]
18:24:29.317 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
18:24:29.321 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 63492; running score is 0.100
18:24:29.321 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=7.6928 known=(45852 @ 2.4660) novel=(22477 @ 2.4146) truthSites(18665 accessible, 16798 called), name=anonymous]
18:24:29.321 INFO VariantRecalibrator - Writing out recalibration table...
18:24:29.624 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=989855744
18:24:29.648 INFO gatk - Initializing VQSR tests/resetting random number generator
18:24:29.661 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:29.661 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:29.662 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:29.662 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:29.662 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:29.662 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:29 PM UTC
18:24:29.662 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:29.662 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:29.662 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:29.662 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:29.662 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:29.662 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:29.662 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:29.663 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:29.663 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:29.663 INFO VariantRecalibrator - Requester pays: disabled
18:24:29.663 INFO VariantRecalibrator - Initializing engine
18:24:29.664 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/chr1snippet.doctoredMQ.sites_only.vcf.gz
18:24:29.684 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/chr1snippet.doctoredMQ.sites_only.vcf.gz
18:24:29.732 INFO IntervalArgumentCollection - Processing 10000000 bp from intervals
18:24:29.748 INFO VariantRecalibrator - Done initializing engine
18:24:29.748 INFO TrainingSet - Found same track: Known = false Training = true Truth = true Prior = Q15.0
18:24:29.761 INFO ProgressMeter - Starting traversal
18:24:29.761 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:29.813 INFO ProgressMeter - chr1:6212018 0.0 2791 3283529.4
18:24:29.813 INFO ProgressMeter - Traversal complete. Processed 2791 total variants in 0.0 minutes.
18:24:29.813 INFO VariantDataManager - AS_QD: mean = 20.88 standard deviation = 8.12
18:24:29.813 INFO VariantDataManager - AS_ReadPosRankSum: mean = -0.05 standard deviation = 0.74
18:24:29.813 INFO VariantDataManager - AS_MQ: mean = 59.82 standard deviation = 2.48
18:24:29.814 INFO VariantDataManager - AS_SOR: mean = 0.86 standard deviation = 0.67
18:24:29.814 INFO VariantDataManager - Annotation order is: [AS_QD, AS_ReadPosRankSum, AS_MQ, AS_SOR]
18:24:29.814 INFO VariantDataManager - Training with 2774 variants after standard deviation thresholding.
18:24:29.814 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:29.842 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:29.858 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.12046
18:24:29.874 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.09714
18:24:29.889 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.07781
18:24:29.905 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.05863
18:24:29.921 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01774
18:24:29.937 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00612
18:24:29.953 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00395
18:24:29.969 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00313
18:24:29.985 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00276
18:24:30.001 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00245
18:24:30.016 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00219
18:24:30.032 INFO VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00198
18:24:30.032 INFO VariantRecalibratorEngine - Convergence after 60 iterations!
18:24:30.033 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
18:24:30.043 INFO VariantDataManager - Selected worst 6 scoring variants --> variants with LOD <= -5.0000.
18:24:30.043 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:30.043 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:30.043 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
18:24:30.043 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
18:24:30.056 INFO TrancheManager - Finding 4 tranches for 2786 variants
18:24:30.057 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
18:24:30.057 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
18:24:30.057 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-39326.4087 known=(0 @ 0.0000) novel=(2786 @ 3.2340) truthSites(2786 accessible, 2786 called), name=anonymous]
18:24:30.057 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
18:24:30.058 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 3; running score is 0.001
18:24:30.058 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-12.9282 known=(0 @ 0.0000) novel=(2783 @ 3.2295) truthSites(2786 accessible, 2783 called), name=anonymous]
18:24:30.058 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
18:24:30.058 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 28; running score is 0.010
18:24:30.058 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=626.3145 known=(0 @ 0.0000) novel=(2758 @ 3.2562) truthSites(2786 accessible, 2758 called), name=anonymous]
18:24:30.058 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
18:24:30.059 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 279; running score is 0.100
18:24:30.059 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=935.3268 known=(0 @ 0.0000) novel=(2507 @ 3.2134) truthSites(2786 accessible, 2507 called), name=anonymous]
18:24:30.059 INFO VariantRecalibrator - Writing out recalibration table...
18:24:30.083 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=989855744
18:24:30.089 INFO gatk - Initializing VQSR tests/resetting random number generator
[May 27, 2025 at 6:24:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=989855744
18:24:32.499 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:32.499 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:32.499 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:32.499 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:32.499 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:32.499 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:32 PM UTC
18:24:32.499 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:32.500 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:32.500 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:32.500 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:32.500 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:32.500 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:32.500 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:32.500 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:32.500 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:32.500 INFO VariantRecalibrator - Requester pays: disabled
18:24:32.500 INFO VariantRecalibrator - Initializing engine
18:24:32.501 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/dbsnp_132_b37.leftAligned.20.1M-10M.vcf
18:24:32.504 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/sites_r27_nr.b37_fwd.20.1M-10M.vcf
18:24:32.506 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf
18:24:32.508 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf
18:24:32.511 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_20_1m_10m_python_2dcnn.indels.vcf.gz
18:24:32.529 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
18:24:32.530 INFO VariantRecalibrator - Done initializing engine
18:24:32.530 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
18:24:32.530 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
18:24:32.530 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
18:24:32.534 INFO ProgressMeter - Starting traversal
18:24:32.534 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:33.528 INFO ProgressMeter - 20:9938789 0.0 134919 8144004.0
18:24:33.528 INFO ProgressMeter - Traversal complete. Processed 134919 total variants in 0.0 minutes.
18:24:33.531 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
18:24:33.534 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
18:24:33.538 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
18:24:33.561 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
18:24:33.562 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
18:24:33.562 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:33.753 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:33.831 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.13181
18:24:33.915 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.46782
18:24:33.980 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 9.04961
18:24:34.047 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.04477
18:24:34.114 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01711
18:24:34.181 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.02053
18:24:34.247 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.01194
18:24:34.314 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01038
18:24:34.381 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.06192
18:24:34.448 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01281
18:24:34.518 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00457
18:24:34.545 INFO VariantRecalibratorEngine - Convergence after 57 iterations!
18:24:34.550 INFO VariantRecalibratorEngine - Evaluating full set of 134603 variants...
18:24:34.670 INFO VariantDataManager - Selected worst 754 scoring variants --> variants with LOD <= -5.0000.
18:24:34.670 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:34.672 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:34.674 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.05287
18:24:34.675 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.02030
18:24:34.676 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.00986
18:24:34.677 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.00749
18:24:34.678 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.00850
18:24:34.680 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.01430
18:24:34.681 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02541
18:24:34.682 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.02173
18:24:34.683 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.01024
18:24:34.685 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00479
18:24:34.686 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00245
18:24:34.686 INFO VariantRecalibratorEngine - Convergence after 57 iterations!
18:24:34.688 INFO VariantRecalibratorEngine - Evaluating full set of 134603 variants...
18:24:34.880 INFO TrancheManager - Finding 4 tranches for 134603 variants
18:24:34.913 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
18:24:34.918 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
18:24:34.918 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-246.6082 known=(61809 @ 2.2991) novel=(72794 @ 2.2239) truthSites(18665 accessible, 18665 called), name=anonymous]
18:24:34.918 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
18:24:34.922 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 649; running score is 0.001
18:24:34.922 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-4.2626 known=(61478 @ 2.3089) novel=(72476 @ 2.2282) truthSites(18665 accessible, 18646 called), name=anonymous]
18:24:34.922 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
18:24:34.927 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 7924; running score is 0.010
18:24:34.927 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=0.6000 known=(59416 @ 2.3515) novel=(67263 @ 2.2813) truthSites(18665 accessible, 18478 called), name=anonymous]
18:24:34.927 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
18:24:34.931 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 52632; running score is 0.100
18:24:34.931 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=4.4668 known=(48943 @ 2.4389) novel=(33028 @ 2.3795) truthSites(18665 accessible, 16798 called), name=anonymous]
18:24:34.931 INFO VariantRecalibrator - Writing out recalibration table...
18:24:35.244 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=989855744
18:24:35.246 INFO gatk - Initializing VQSR tests/resetting random number generator
18:24:35.254 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:35.254 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:35.254 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:35.254 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:35.255 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:35.255 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:35 PM UTC
18:24:35.255 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:35.255 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:35.255 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:35.255 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:35.255 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:35.255 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:35.255 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:35.255 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:35.255 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:35.255 INFO VariantRecalibrator - Requester pays: disabled
18:24:35.255 INFO VariantRecalibrator - Initializing engine
18:24:35.256 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/dbsnp_132_b37.leftAligned.20.1M-10M.vcf
18:24:35.259 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/sites_r27_nr.b37_fwd.20.1M-10M.vcf
18:24:35.261 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf
18:24:35.263 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf
18:24:35.267 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
18:24:35.268 INFO VariantRecalibrator - Done initializing engine
18:24:35.268 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
18:24:35.268 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
18:24:35.268 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
18:24:35.269 INFO ProgressMeter - Starting traversal
18:24:35.270 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:36.237 INFO ProgressMeter - 20:9944766 0.0 131821 8179172.7
18:24:36.237 INFO ProgressMeter - Traversal complete. Processed 131821 total variants in 0.0 minutes.
18:24:36.239 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
18:24:36.242 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
18:24:36.244 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
18:24:36.266 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
18:24:36.267 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
18:24:36.268 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:36.505 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:36.608 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.42302
18:24:36.712 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24203
18:24:36.816 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15214
18:24:36.922 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.22858
18:24:37.030 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07799
18:24:37.137 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04227
18:24:37.239 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00976
18:24:37.328 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03859
18:24:37.415 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.18953
18:24:37.503 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01049
18:24:37.574 INFO VariantRecalibratorEngine - Convergence after 54 iterations!
18:24:37.580 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
18:24:37.648 INFO VariantDataManager - Selected worst 474 scoring variants --> variants with LOD <= -5.0000.
18:24:37.648 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:37.649 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:37.650 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
18:24:37.651 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
18:24:37.828 INFO TrancheManager - Finding 12 tranches for 131821 variants
18:24:37.864 INFO TrancheManager - VQSLODTranche threshold 10.00 => selection metric threshold 0.900
18:24:37.872 INFO TrancheManager - Found tranche for 10.000: 0.900 threshold starting with variant 97819; running score is 0.262
18:24:37.873 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=10.0000 known=(29048 @ 2.5026) novel=(4954 @ 2.3633) truthSites(18665 accessible, 13780 called), name=anonymous]
18:24:37.873 INFO TrancheManager - VQSLODTranche threshold 8.00 => selection metric threshold 0.920
18:24:37.877 INFO TrancheManager - Found tranche for 8.000: 0.920 threshold starting with variant 68875; running score is 0.114
18:24:37.877 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=8.0000 known=(44004 @ 2.4829) novel=(18942 @ 2.4147) truthSites(18665 accessible, 16543 called), name=anonymous]
18:24:37.878 INFO TrancheManager - VQSLODTranche threshold 6.00 => selection metric threshold 0.940
18:24:37.882 INFO TrancheManager - Found tranche for 6.000: 0.940 threshold starting with variant 34094; running score is 0.052
18:24:37.882 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=6.0000 known=(52474 @ 2.4242) novel=(45253 @ 2.3994) truthSites(18665 accessible, 17701 called), name=anonymous]
18:24:37.882 INFO TrancheManager - VQSLODTranche threshold 4.00 => selection metric threshold 0.960
18:24:37.886 INFO TrancheManager - Found tranche for 4.000: 0.960 threshold starting with variant 12275; running score is 0.023
18:24:37.886 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=4.0000 known=(56181 @ 2.3913) novel=(63365 @ 2.3212) truthSites(18665 accessible, 18243 called), name=anonymous]
18:24:37.887 INFO TrancheManager - VQSLODTranche threshold 2.00 => selection metric threshold 0.980
18:24:37.891 INFO TrancheManager - Found tranche for 2.000: 0.980 threshold starting with variant 4952; running score is 0.009
18:24:37.891 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=2.0000 known=(57758 @ 2.3573) novel=(69111 @ 2.2722) truthSites(18665 accessible, 18502 called), name=anonymous]
18:24:37.891 INFO TrancheManager - VQSLODTranche threshold 0.00 => selection metric threshold 1.000
18:24:37.895 INFO TrancheManager - Found tranche for 0.000: 1.000 threshold starting with variant 2260; running score is 0.004
18:24:37.895 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=0.0000 known=(58579 @ 2.3306) novel=(70982 @ 2.2511) truthSites(18665 accessible, 18598 called), name=anonymous]
18:24:37.895 INFO TrancheManager - VQSLODTranche threshold -2.00 => selection metric threshold 1.020
18:24:37.900 INFO TrancheManager - Found tranche for -2.000: 1.020 threshold starting with variant 1099; running score is 0.001
18:24:37.900 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-2.0000 known=(59019 @ 2.3111) novel=(71703 @ 2.2372) truthSites(18665 accessible, 18640 called), name=anonymous]
18:24:37.900 INFO TrancheManager - VQSLODTranche threshold -4.00 => selection metric threshold 1.040
18:24:37.904 INFO TrancheManager - Found tranche for -4.000: 1.040 threshold starting with variant 606; running score is 0.001
18:24:37.904 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-4.0000 known=(59205 @ 2.3054) novel=(72010 @ 2.2272) truthSites(18665 accessible, 18648 called), name=anonymous]
18:24:37.904 INFO TrancheManager - VQSLODTranche threshold -6.00 => selection metric threshold 1.060
18:24:37.909 INFO TrancheManager - Found tranche for -6.000: 1.060 threshold starting with variant 429; running score is 0.001
18:24:37.909 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-6.0000 known=(59292 @ 2.3026) novel=(72100 @ 2.2261) truthSites(18665 accessible, 18653 called), name=anonymous]
18:24:37.909 INFO TrancheManager - VQSLODTranche threshold -8.00 => selection metric threshold 1.080
18:24:37.913 INFO TrancheManager - Found tranche for -8.000: 1.080 threshold starting with variant 314; running score is 0.000
18:24:37.913 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-8.0000 known=(59355 @ 2.3009) novel=(72152 @ 2.2247) truthSites(18665 accessible, 18657 called), name=anonymous]
18:24:37.913 INFO TrancheManager - VQSLODTranche threshold -10.00 => selection metric threshold 1.100
18:24:37.917 INFO TrancheManager - Found tranche for -10.000: 1.100 threshold starting with variant 264; running score is 0.000
18:24:37.917 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-10.0000 known=(59372 @ 2.3008) novel=(72185 @ 2.2246) truthSites(18665 accessible, 18658 called), name=anonymous]
18:24:37.917 INFO TrancheManager - VQSLODTranche threshold -12.00 => selection metric threshold 1.120
18:24:37.922 INFO TrancheManager - Found tranche for -12.000: 1.120 threshold starting with variant 211; running score is 0.000
18:24:37.922 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-12.0000 known=(59394 @ 2.3004) novel=(72216 @ 2.2244) truthSites(18665 accessible, 18659 called), name=anonymous]
18:24:37.922 INFO VariantRecalibrator - Writing out recalibration table...
18:24:38.225 INFO VariantRecalibrator - Tranches plot will not be generated since we are running in scattered mode
18:24:38.230 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=989855744
18:24:38.253 INFO gatk - Initializing VQSR tests/resetting random number generator
[May 27, 2025 at 6:24:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=989855744
18:24:39.810 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:39.810 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:39.810 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:39.811 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:39.811 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:39.811 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:39 PM UTC
18:24:39.811 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:39.811 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:39.811 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:39.811 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:39.811 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:39.811 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:39.811 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:39.811 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:39.811 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:39.811 INFO VariantRecalibrator - Requester pays: disabled
18:24:39.811 INFO VariantRecalibrator - Initializing engine
18:24:39.813 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/chr1snippet.doctoredMQ.sites_only.vcf.gz
18:24:39.829 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/chr1snippet.doctoredMQ.sites_only.vcf.gz
18:24:39.888 INFO IntervalArgumentCollection - Processing 10000000 bp from intervals
18:24:39.911 INFO VariantRecalibrator - Done initializing engine
18:24:39.912 INFO TrainingSet - Found same track: Known = false Training = true Truth = true Prior = Q15.0
18:24:39.930 INFO ProgressMeter - Starting traversal
18:24:39.930 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:40.009 INFO ProgressMeter - chr1:6212018 0.0 2791 2119746.8
18:24:40.009 INFO ProgressMeter - Traversal complete. Processed 2791 total variants in 0.0 minutes.
18:24:40.010 INFO VariantDataManager - AS_QD: mean = 20.88 standard deviation = 8.12
18:24:40.010 INFO VariantDataManager - AS_ReadPosRankSum: mean = -0.05 standard deviation = 0.74
18:24:40.010 INFO VariantDataManager - AS_MQ: mean = 59.82 standard deviation = 2.48
18:24:40.010 INFO VariantDataManager - AS_SOR: mean = 0.86 standard deviation = 0.67
18:24:40.010 INFO VariantDataManager - AS_FS: mean = 1.08 standard deviation = 2.43
18:24:40.010 INFO VariantDataManager - AS_MQRankSum: mean = 0.00 standard deviation = 0.01
18:24:40.011 INFO VariantDataManager - Annotation order is: [AS_QD, AS_ReadPosRankSum, AS_MQ, AS_SOR, AS_FS, AS_MQRankSum]
18:24:40.011 INFO VariantDataManager - Training with 2769 variants after standard deviation thresholding.
18:24:40.011 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:40.044 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:40.068 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.56007
18:24:40.092 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.67355
18:24:40.117 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 5.08559
18:24:40.141 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.01567
18:24:40.167 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.02021
18:24:40.192 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.01989
18:24:40.216 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02504
18:24:40.241 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03657
18:24:40.266 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.04057
18:24:40.291 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.08648
18:24:40.317 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.01514
18:24:40.347 INFO VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00496
18:24:40.371 INFO VariantRecalibratorEngine - Finished iteration 65. Current change in mixture coefficients = 0.00163
18:24:40.371 INFO VariantRecalibratorEngine - Convergence after 65 iterations!
18:24:40.373 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
18:24:40.393 INFO VariantDataManager - Selected worst 5 scoring variants --> variants with LOD <= -5.0000.
18:24:40.393 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:40.393 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:40.393 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
18:24:40.394 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
18:24:40.407 INFO TrancheManager - Finding 4 tranches for 2786 variants
18:24:40.408 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
18:24:40.408 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
18:24:40.408 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-39314.8821 known=(0 @ 0.0000) novel=(2786 @ 3.2340) truthSites(2786 accessible, 2786 called), name=anonymous]
18:24:40.408 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
18:24:40.408 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 3; running score is 0.001
18:24:40.408 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-16.8308 known=(0 @ 0.0000) novel=(2783 @ 3.2295) truthSites(2786 accessible, 2783 called), name=anonymous]
18:24:40.408 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
18:24:40.408 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 28; running score is 0.010
18:24:40.408 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=1239951.3360 known=(0 @ 0.0000) novel=(2758 @ 3.2496) truthSites(2786 accessible, 2758 called), name=anonymous]
18:24:40.409 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
18:24:40.409 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 279; running score is 0.100
18:24:40.409 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=2091223.5520 known=(0 @ 0.0000) novel=(2507 @ 3.2205) truthSites(2786 accessible, 2507 called), name=anonymous]
18:24:40.409 INFO VariantRecalibrator - Writing out recalibration table...
18:24:40.425 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=989855744
18:24:40.426 INFO gatk - Initializing VQSR tests/resetting random number generator
[May 27, 2025 at 6:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=989855744
[May 27, 2025 at 6:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[May 27, 2025 at 6:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[May 27, 2025 at 6:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=989855744
[May 27, 2025 at 6:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=989855744
[May 27, 2025 at 6:24:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=989855744
18:24:45.470 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:45.470 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:45.470 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:45.470 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:45.470 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:45.471 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:45 PM UTC
18:24:45.471 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:45.471 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:45.471 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:45.471 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:45.471 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:45.471 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:45.471 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:45.471 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:45.471 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:45.471 INFO VariantRecalibrator - Requester pays: disabled
18:24:45.471 INFO VariantRecalibrator - Initializing engine
18:24:45.472 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/dbsnp_132_b37.leftAligned.20.1M-10M.vcf
18:24:45.474 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/sites_r27_nr.b37_fwd.20.1M-10M.vcf
18:24:45.476 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf
18:24:45.477 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf
18:24:45.479 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
18:24:45.480 INFO VariantRecalibrator - Done initializing engine
18:24:45.480 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
18:24:45.480 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
18:24:45.480 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
18:24:45.481 INFO ProgressMeter - Starting traversal
18:24:45.481 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:46.439 INFO ProgressMeter - 20:9944766 0.0 131821 8256012.5
18:24:46.439 INFO ProgressMeter - Traversal complete. Processed 131821 total variants in 0.0 minutes.
18:24:46.441 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
18:24:46.445 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
18:24:46.448 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
18:24:46.469 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
18:24:46.470 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
18:24:46.470 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:46.708 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:46.813 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.42302
18:24:46.896 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24203
18:24:46.982 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15214
18:24:47.071 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.22858
18:24:47.191 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07799
18:24:47.281 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04227
18:24:47.370 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00976
18:24:47.459 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03859
18:24:47.548 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.18953
18:24:47.645 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01049
18:24:47.715 INFO VariantRecalibratorEngine - Convergence after 54 iterations!
18:24:47.722 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
18:24:47.794 INFO VariantDataManager - Selected worst 474 scoring variants --> variants with LOD <= -5.0000.
18:24:47.794 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:47.795 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:47.796 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
18:24:47.796 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
18:24:47.978 INFO TrancheManager - Finding 12 tranches for 131821 variants
18:24:48.010 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
18:24:48.014 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
18:24:48.014 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-240.7209 known=(59500 @ 2.2991) novel=(72321 @ 2.2239) truthSites(18665 accessible, 18665 called), name=anonymous]
18:24:48.014 INFO TrancheManager - TruthSensitivityTranche threshold 99.95 => selection metric threshold 0.000
18:24:48.019 INFO TrancheManager - Found tranche for 99.950: 0.000 threshold starting with variant 381; running score is 0.001
18:24:48.019 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.95 minVQSLod=-6.6729 known=(59316 @ 2.3020) novel=(72124 @ 2.2259) truthSites(18665 accessible, 18655 called), name=anonymous]
18:24:48.019 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
18:24:48.026 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 747; running score is 0.001
18:24:48.026 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-3.1318 known=(59151 @ 2.3066) novel=(71923 @ 2.2295) truthSites(18665 accessible, 18646 called), name=anonymous]
18:24:48.026 INFO TrancheManager - TruthSensitivityTranche threshold 99.80 => selection metric threshold 0.002
18:24:48.033 INFO TrancheManager - Found tranche for 99.800: 0.002 threshold starting with variant 1480; running score is 0.002
18:24:48.033 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.80 minVQSLod=-1.1986 known=(58885 @ 2.3181) novel=(71456 @ 2.2416) truthSites(18665 accessible, 18627 called), name=anonymous]
18:24:48.033 INFO TrancheManager - TruthSensitivityTranche threshold 99.60 => selection metric threshold 0.004
18:24:48.038 INFO TrancheManager - Found tranche for 99.600: 0.004 threshold starting with variant 2377; running score is 0.004
18:24:48.038 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.60 minVQSLod=0.1656 known=(58528 @ 2.3328) novel=(70916 @ 2.2530) truthSites(18665 accessible, 18590 called), name=anonymous]
18:24:48.038 INFO TrancheManager - TruthSensitivityTranche threshold 99.50 => selection metric threshold 0.005
18:24:48.042 INFO TrancheManager - Found tranche for 99.500: 0.005 threshold starting with variant 3042; running score is 0.005
18:24:48.042 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.50 minVQSLod=0.9426 known=(58256 @ 2.3427) novel=(70523 @ 2.2598) truthSites(18665 accessible, 18571 called), name=anonymous]
18:24:48.042 INFO TrancheManager - TruthSensitivityTranche threshold 99.40 => selection metric threshold 0.006
18:24:48.046 INFO TrancheManager - Found tranche for 99.400: 0.006 threshold starting with variant 3577; running score is 0.006
18:24:48.046 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.40 minVQSLod=1.3251 known=(58072 @ 2.3504) novel=(70172 @ 2.2640) truthSites(18665 accessible, 18553 called), name=anonymous]
18:24:48.046 INFO TrancheManager - TruthSensitivityTranche threshold 99.30 => selection metric threshold 0.007
18:24:48.050 INFO TrancheManager - Found tranche for 99.300: 0.007 threshold starting with variant 4004; running score is 0.007
18:24:48.050 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.30 minVQSLod=1.5909 known=(57947 @ 2.3539) novel=(69870 @ 2.2668) truthSites(18665 accessible, 18534 called), name=anonymous]
18:24:48.050 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
18:24:48.057 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 5604; running score is 0.010
18:24:48.057 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=2.2535 known=(57628 @ 2.3617) novel=(68589 @ 2.2769) truthSites(18665 accessible, 18478 called), name=anonymous]
18:24:48.057 INFO TrancheManager - TruthSensitivityTranche threshold 98.00 => selection metric threshold 0.020
18:24:48.061 INFO TrancheManager - Found tranche for 98.000: 0.020 threshold starting with variant 10673; running score is 0.020
18:24:48.061 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=98.00 minVQSLod=3.7431 known=(56497 @ 2.3862) novel=(64651 @ 2.3078) truthSites(18665 accessible, 18291 called), name=anonymous]
18:24:48.061 INFO TrancheManager - TruthSensitivityTranche threshold 97.00 => selection metric threshold 0.030
18:24:48.068 INFO TrancheManager - Found tranche for 97.000: 0.030 threshold starting with variant 16985; running score is 0.030
18:24:48.068 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=97.00 minVQSLod=4.6404 known=(55330 @ 2.4003) novel=(59506 @ 2.3526) truthSites(18665 accessible, 18105 called), name=anonymous]
18:24:48.068 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
18:24:48.075 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 63492; running score is 0.100
18:24:48.075 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=7.6928 known=(45852 @ 2.4660) novel=(22477 @ 2.4146) truthSites(18665 accessible, 16798 called), name=anonymous]
18:24:48.075 INFO VariantRecalibrator - Writing out recalibration table...
18:24:48.372 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=989855744
18:24:48.394 INFO gatk - Initializing VQSR tests/resetting random number generator
18:24:48.401 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:48.401 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
18:24:48.401 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:24:48.401 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
18:24:48.401 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
18:24:48.401 INFO VariantRecalibrator - Start Date/Time: May 27, 2025 at 6:24:48 PM UTC
18:24:48.401 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:48.401 INFO VariantRecalibrator - ------------------------------------------------------------
18:24:48.402 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:24:48.402 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:24:48.402 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:24:48.402 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:24:48.402 INFO VariantRecalibrator - Deflater: IntelDeflater
18:24:48.402 INFO VariantRecalibrator - Inflater: IntelInflater
18:24:48.402 INFO VariantRecalibrator - GCS max retries/reopens: 20
18:24:48.402 INFO VariantRecalibrator - Requester pays: disabled
18:24:48.402 INFO VariantRecalibrator - Initializing engine
18:24:48.403 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/chr1snippet.doctoredMQ.sites_only.vcf.gz
18:24:48.413 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/large/VQSR/chr1snippet.doctoredMQ.sites_only.vcf.gz
18:24:48.445 INFO IntervalArgumentCollection - Processing 10000000 bp from intervals
18:24:48.461 INFO VariantRecalibrator - Done initializing engine
18:24:48.461 INFO TrainingSet - Found same track: Known = false Training = true Truth = true Prior = Q15.0
18:24:48.471 INFO ProgressMeter - Starting traversal
18:24:48.471 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:24:48.513 INFO ProgressMeter - chr1:6212018 0.0 2791 4084390.2
18:24:48.513 INFO ProgressMeter - Traversal complete. Processed 2791 total variants in 0.0 minutes.
18:24:48.513 INFO VariantDataManager - AS_QD: mean = 20.88 standard deviation = 8.12
18:24:48.513 INFO VariantDataManager - AS_ReadPosRankSum: mean = -0.05 standard deviation = 0.74
18:24:48.513 INFO VariantDataManager - AS_MQ: mean = 59.82 standard deviation = 2.48
18:24:48.513 INFO VariantDataManager - AS_SOR: mean = 0.86 standard deviation = 0.67
18:24:48.514 INFO VariantDataManager - Annotation order is: [AS_QD, AS_ReadPosRankSum, AS_MQ, AS_SOR]
18:24:48.514 INFO VariantDataManager - Training with 2774 variants after standard deviation thresholding.
18:24:48.514 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:48.543 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:48.559 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.12046
18:24:48.576 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.09714
18:24:48.592 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.07781
18:24:48.608 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.05863
18:24:48.625 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01774
18:24:48.641 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00612
18:24:48.657 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00395
18:24:48.673 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00313
18:24:48.690 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00276
18:24:48.706 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00245
18:24:48.722 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00219
18:24:48.739 INFO VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00198
18:24:48.739 INFO VariantRecalibratorEngine - Convergence after 60 iterations!
18:24:48.740 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
18:24:48.749 INFO VariantDataManager - Selected worst 6 scoring variants --> variants with LOD <= -5.0000.
18:24:48.749 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
18:24:48.749 INFO VariantRecalibratorEngine - Finished iteration 0.
18:24:48.749 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
18:24:48.749 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
18:24:48.757 INFO TrancheManager - Finding 12 tranches for 2786 variants
18:24:48.758 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
18:24:48.758 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
18:24:48.758 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-39326.4087 known=(0 @ 0.0000) novel=(2786 @ 3.2340) truthSites(2786 accessible, 2786 called), name=anonymous]
18:24:48.758 INFO TrancheManager - TruthSensitivityTranche threshold 99.95 => selection metric threshold 0.000
18:24:48.758 INFO TrancheManager - Found tranche for 99.950: 0.000 threshold starting with variant 2; running score is 0.001
18:24:48.758 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.95 minVQSLod=-22753.7269 known=(0 @ 0.0000) novel=(2784 @ 3.2310) truthSites(2786 accessible, 2784 called), name=anonymous]
18:24:48.759 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
18:24:48.759 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 3; running score is 0.001
18:24:48.759 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-12.9282 known=(0 @ 0.0000) novel=(2783 @ 3.2295) truthSites(2786 accessible, 2783 called), name=anonymous]
18:24:48.759 INFO TrancheManager - TruthSensitivityTranche threshold 99.80 => selection metric threshold 0.002
18:24:48.759 INFO TrancheManager - Found tranche for 99.800: 0.002 threshold starting with variant 6; running score is 0.002
18:24:48.759 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.80 minVQSLod=-5.7548 known=(0 @ 0.0000) novel=(2780 @ 3.2314) truthSites(2786 accessible, 2780 called), name=anonymous]
18:24:48.759 INFO TrancheManager - TruthSensitivityTranche threshold 99.60 => selection metric threshold 0.004
18:24:48.759 INFO TrancheManager - Found tranche for 99.600: 0.004 threshold starting with variant 12; running score is 0.004
18:24:48.759 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.60 minVQSLod=250.6941 known=(0 @ 0.0000) novel=(2774 @ 3.2481) truthSites(2786 accessible, 2774 called), name=anonymous]
18:24:48.759 INFO TrancheManager - TruthSensitivityTranche threshold 99.50 => selection metric threshold 0.005
18:24:48.759 INFO TrancheManager - Found tranche for 99.500: 0.005 threshold starting with variant 14; running score is 0.005
18:24:48.759 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.50 minVQSLod=342.2903 known=(0 @ 0.0000) novel=(2772 @ 3.2515) truthSites(2786 accessible, 2772 called), name=anonymous]
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche threshold 99.40 => selection metric threshold 0.006
18:24:48.760 INFO TrancheManager - Found tranche for 99.400: 0.006 threshold starting with variant 17; running score is 0.006
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.40 minVQSLod=511.3402 known=(0 @ 0.0000) novel=(2769 @ 3.2469) truthSites(2786 accessible, 2769 called), name=anonymous]
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche threshold 99.30 => selection metric threshold 0.007
18:24:48.760 INFO TrancheManager - Found tranche for 99.300: 0.007 threshold starting with variant 20; running score is 0.007
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.30 minVQSLod=573.6691 known=(0 @ 0.0000) novel=(2766 @ 3.2423) truthSites(2786 accessible, 2766 called), name=anonymous]
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
18:24:48.760 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 28; running score is 0.010
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=626.3145 known=(0 @ 0.0000) novel=(2758 @ 3.2562) truthSites(2786 accessible, 2758 called), name=anonymous]
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche threshold 98.00 => selection metric threshold 0.020
18:24:48.760 INFO TrancheManager - Found tranche for 98.000: 0.020 threshold starting with variant 56; running score is 0.020
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=98.00 minVQSLod=710.0883 known=(0 @ 0.0000) novel=(2730 @ 3.2523) truthSites(2786 accessible, 2730 called), name=anonymous]
18:24:48.760 INFO TrancheManager - TruthSensitivityTranche threshold 97.00 => selection metric threshold 0.030
18:24:48.761 INFO TrancheManager - Found tranche for 97.000: 0.030 threshold starting with variant 84; running score is 0.030
18:24:48.761 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=97.00 minVQSLod=758.5107 known=(0 @ 0.0000) novel=(2702 @ 3.2484) truthSites(2786 accessible, 2702 called), name=anonymous]
18:24:48.761 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
18:24:48.761 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 279; running score is 0.100
18:24:48.761 INFO TrancheManager - TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=935.3268 known=(0 @ 0.0000) novel=(2507 @ 3.2134) truthSites(2786 accessible, 2507 called), name=anonymous]
18:24:48.761 INFO VariantRecalibrator - Writing out recalibration table...
18:24:48.774 INFO VariantRecalibrator - Shutting down engine
[May 27, 2025 at 6:24:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=989855744
[May 27, 2025 at 6:25:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1728053248