[May 19, 2025 at 7:08:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=685768704
19:08:35.275 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:35.276 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:08:35.276 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:08:35.276 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:08:35.276 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:08:35.276 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:08:35 PM UTC
19:08:35.276 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:35.277 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:35.277 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:08:35.277 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:08:35.277 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:08:35.277 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:08:35.277 INFO VariantRecalibrator - Deflater: IntelDeflater
19:08:35.277 INFO VariantRecalibrator - Inflater: IntelInflater
19:08:35.277 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:08:35.277 INFO VariantRecalibrator - Requester pays: disabled
19:08:35.277 INFO VariantRecalibrator - Initializing engine
19:08:35.281 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
19:08:35.313 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
19:08:35.406 INFO IntervalArgumentCollection - Processing 10000000 bp from intervals
19:08:35.440 INFO VariantRecalibrator - Done initializing engine
19:08:35.440 INFO TrainingSet - Found same track: Known = false Training = true Truth = true Prior = Q15.0
19:08:35.477 INFO ProgressMeter - Starting traversal
19:08:35.478 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:08:35.630 INFO ProgressMeter - chr1:6212018 0.0 2791 1101710.5
19:08:35.631 INFO ProgressMeter - Traversal complete. Processed 2791 total variants in 0.0 minutes.
19:08:35.631 INFO VariantDataManager - AS_QD: mean = 20.88 standard deviation = 8.12
19:08:35.632 INFO VariantDataManager - AS_ReadPosRankSum: mean = -0.05 standard deviation = 0.74
19:08:35.633 INFO VariantDataManager - AS_MQ: mean = 59.82 standard deviation = 2.48
19:08:35.634 INFO VariantDataManager - AS_SOR: mean = 0.86 standard deviation = 0.67
19:08:35.635 INFO VariantDataManager - AS_FS: mean = 1.08 standard deviation = 2.43
19:08:35.636 INFO VariantDataManager - AS_MQRankSum: mean = 0.00 standard deviation = 0.01
19:08:35.648 INFO VariantDataManager - Annotation order is: [AS_QD, AS_ReadPosRankSum, AS_MQ, AS_SOR, AS_FS, AS_MQRankSum]
19:08:35.648 INFO VariantDataManager - Training with 2769 variants after standard deviation thresholding.
19:08:35.648 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:35.704 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:35.742 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.56007
19:08:35.772 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.67355
19:08:35.800 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 5.08559
19:08:35.827 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.01567
19:08:35.862 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.02021
19:08:35.887 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.01989
19:08:35.912 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02504
19:08:35.936 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03657
19:08:35.961 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.04057
19:08:35.986 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.08648
19:08:36.011 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.01514
19:08:36.035 INFO VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00496
19:08:36.059 INFO VariantRecalibratorEngine - Finished iteration 65. Current change in mixture coefficients = 0.00163
19:08:36.059 INFO VariantRecalibratorEngine - Convergence after 65 iterations!
19:08:36.062 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
19:08:36.093 INFO VariantDataManager - Selected worst 5 scoring variants --> variants with LOD <= -5.0000.
19:08:36.093 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:36.093 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:36.094 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
19:08:36.094 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
19:08:36.112 INFO TrancheManager - Finding 4 tranches for 2786 variants
19:08:36.113 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
19:08:36.114 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
19:08:36.114 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]
19:08:36.114 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
19:08:36.114 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 3; running score is 0.001
19:08:36.115 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]
19:08:36.115 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
19:08:36.115 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 28; running score is 0.010
19:08:36.115 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]
19:08:36.115 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
19:08:36.116 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 279; running score is 0.100
19:08:36.116 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]
19:08:36.117 INFO VariantRecalibrator - Writing out recalibration table...
19:08:36.158 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:08:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=685768704
19:08:36.160 INFO gatk - Initializing VQSR tests/resetting random number generator
[May 19, 2025 at 7:08:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=840957952
[May 19, 2025 at 7:08:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=840957952
19:08:41.989 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:41.989 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:08:41.989 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:08:41.990 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:08:41.990 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:08:41.990 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:08:41 PM UTC
19:08:41.990 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:41.990 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:41.990 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:08:41.990 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:08:41.990 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:08:41.990 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:08:41.990 INFO VariantRecalibrator - Deflater: IntelDeflater
19:08:41.991 INFO VariantRecalibrator - Inflater: IntelInflater
19:08:41.991 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:08:41.991 INFO VariantRecalibrator - Requester pays: disabled
19:08:41.991 INFO VariantRecalibrator - Initializing engine
19:08:41.992 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
19:08:42.011 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
19:08:42.064 INFO IntervalArgumentCollection - Processing 10000000 bp from intervals
19:08:42.080 INFO VariantRecalibrator - Done initializing engine
19:08:42.081 INFO TrainingSet - Found same track: Known = false Training = true Truth = true Prior = Q15.0
19:08:42.093 INFO ProgressMeter - Starting traversal
19:08:42.094 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:08:42.139 INFO ProgressMeter - chr1:6212018 0.0 2791 3721333.3
19:08:42.139 INFO ProgressMeter - Traversal complete. Processed 2791 total variants in 0.0 minutes.
19:08:42.140 INFO VariantDataManager - AS_QD: mean = 20.88 standard deviation = 8.12
19:08:42.140 INFO VariantDataManager - AS_ReadPosRankSum: mean = -0.05 standard deviation = 0.74
19:08:42.140 INFO VariantDataManager - AS_MQ: mean = 59.82 standard deviation = 2.48
19:08:42.141 INFO VariantDataManager - AS_SOR: mean = 0.86 standard deviation = 0.67
19:08:42.141 INFO VariantDataManager - Annotation order is: [AS_QD, AS_ReadPosRankSum, AS_MQ, AS_SOR]
19:08:42.142 INFO VariantDataManager - Training with 2774 variants after standard deviation thresholding.
19:08:42.142 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:42.176 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:42.193 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.16919
19:08:42.211 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.14268
19:08:42.228 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.19617
19:08:42.246 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.09047
19:08:42.263 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.05235
19:08:42.280 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04028
19:08:42.297 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02103
19:08:42.314 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01461
19:08:42.332 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.01136
19:08:42.349 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00583
19:08:42.370 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00291
19:08:42.379 INFO VariantRecalibratorEngine - Convergence after 58 iterations!
19:08:42.381 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
19:08:42.389 INFO VariantDataManager - Selected worst 0 scoring variants --> variants with LOD <= -5.5000.
19:08:42.393 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:08:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=840957952
19:08:42.395 INFO gatk - Initializing VQSR tests/resetting random number generator
[May 19, 2025 at 7:08:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=840957952
[May 19, 2025 at 7:08:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=840957952
[May 19, 2025 at 7:08:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=840957952
[May 19, 2025 at 7:08:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=840957952
19:08:45.390 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:45.391 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:08:45.391 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:08:45.391 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:08:45.391 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:08:45.391 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:08:45 PM UTC
19:08:45.391 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:45.391 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:45.391 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:08:45.391 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:08:45.392 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:08:45.392 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:08:45.392 INFO VariantRecalibrator - Deflater: IntelDeflater
19:08:45.392 INFO VariantRecalibrator - Inflater: IntelInflater
19:08:45.392 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:08:45.392 INFO VariantRecalibrator - Requester pays: disabled
19:08:45.392 INFO VariantRecalibrator - Initializing engine
19:08:45.393 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
19:08:45.396 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
19:08:45.398 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
19:08:45.400 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
19:08:45.403 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
19:08:45.404 INFO VariantRecalibrator - Done initializing engine
19:08:45.406 WARN VariantDataManager - Ignoring duplicate annotations for recalibration [HRun]
19:08:45.407 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
19:08:45.407 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
19:08:45.407 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
19:08:45.408 INFO ProgressMeter - Starting traversal
19:08:45.408 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:08:46.415 INFO ProgressMeter - 20:9944766 0.0 131821 7854280.0
19:08:46.415 INFO ProgressMeter - Traversal complete. Processed 131821 total variants in 0.0 minutes.
19:08:46.418 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
19:08:46.423 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
19:08:46.427 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
19:08:46.459 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
19:08:46.460 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
19:08:46.461 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:46.707 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:46.808 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.42302
19:08:46.910 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24203
19:08:47.014 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15214
19:08:47.120 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.22858
19:08:47.227 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07799
19:08:47.335 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04227
19:08:47.447 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00976
19:08:47.536 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03859
19:08:47.625 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.18953
19:08:47.715 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01049
19:08:47.787 INFO VariantRecalibratorEngine - Convergence after 54 iterations!
19:08:47.794 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
19:08:47.860 INFO VariantDataManager - Selected worst 474 scoring variants --> variants with LOD <= -5.0000.
19:08:47.861 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:47.862 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:47.863 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
19:08:47.864 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
19:08:48.044 INFO TrancheManager - Finding 4 tranches for 131821 variants
19:08:48.077 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
19:08:48.081 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
19:08:48.081 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]
19:08:48.081 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
19:08:48.085 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 747; running score is 0.001
19:08:48.085 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]
19:08:48.086 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
19:08:48.090 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 5604; running score is 0.010
19:08:48.090 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]
19:08:48.090 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
19:08:48.094 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 63492; running score is 0.100
19:08:48.094 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]
19:08:48.095 INFO VariantRecalibrator - Writing out recalibration table...
19:08:48.404 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:08:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=840957952
19:08:48.436 INFO gatk - Initializing VQSR tests/resetting random number generator
19:08:48.444 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:48.444 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:08:48.444 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:08:48.444 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:08:48.444 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:08:48.445 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:08:48 PM UTC
19:08:48.445 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:48.445 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:48.445 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:08:48.445 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:08:48.445 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:08:48.445 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:08:48.445 INFO VariantRecalibrator - Deflater: IntelDeflater
19:08:48.445 INFO VariantRecalibrator - Inflater: IntelInflater
19:08:48.445 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:08:48.445 INFO VariantRecalibrator - Requester pays: disabled
19:08:48.446 INFO VariantRecalibrator - Initializing engine
19:08:48.446 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
19:08:48.448 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
19:08:48.450 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
19:08:48.451 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
19:08:48.453 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
19:08:48.454 INFO VariantRecalibrator - Done initializing engine
19:08:48.454 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
19:08:48.454 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
19:08:48.454 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
19:08:48.455 INFO ProgressMeter - Starting traversal
19:08:48.455 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:08:49.431 INFO ProgressMeter - 20:9944766 0.0 131821 8103750.0
19:08:49.431 INFO ProgressMeter - Traversal complete. Processed 131821 total variants in 0.0 minutes.
19:08:49.434 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
19:08:49.439 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
19:08:49.443 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
19:08:49.468 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
19:08:49.470 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
19:08:49.470 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:49.734 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:49.840 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.42302
19:08:49.952 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24203
19:08:50.038 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15214
19:08:50.126 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.22858
19:08:50.214 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07799
19:08:50.301 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04227
19:08:50.390 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00976
19:08:50.479 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03859
19:08:50.568 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.18953
19:08:50.657 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01049
19:08:50.736 INFO VariantRecalibratorEngine - Convergence after 54 iterations!
19:08:50.744 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
19:08:50.815 INFO VariantDataManager - Selected worst 474 scoring variants --> variants with LOD <= -5.0000.
19:08:50.815 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:50.816 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:50.817 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
19:08:50.819 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
19:08:51.004 INFO TrancheManager - Finding 4 tranches for 131821 variants
19:08:51.037 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
19:08:51.042 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
19:08:51.042 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]
19:08:51.042 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
19:08:51.047 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 747; running score is 0.001
19:08:51.047 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]
19:08:51.048 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
19:08:51.052 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 5604; running score is 0.010
19:08:51.052 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]
19:08:51.052 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
19:08:51.057 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 63492; running score is 0.100
19:08:51.057 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]
19:08:51.057 INFO VariantRecalibrator - Writing out recalibration table...
19:08:51.363 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:08:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=954204160
19:08:51.385 INFO gatk - Initializing VQSR tests/resetting random number generator
19:08:51.393 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:51.394 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:08:51.394 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:08:51.394 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:08:51.394 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:08:51.394 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:08:51 PM UTC
19:08:51.394 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:51.394 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:51.394 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:08:51.394 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:08:51.394 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:08:51.394 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:08:51.394 INFO VariantRecalibrator - Deflater: IntelDeflater
19:08:51.394 INFO VariantRecalibrator - Inflater: IntelInflater
19:08:51.394 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:08:51.395 INFO VariantRecalibrator - Requester pays: disabled
19:08:51.395 INFO VariantRecalibrator - Initializing engine
19:08:51.396 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
19:08:51.406 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
19:08:51.440 INFO IntervalArgumentCollection - Processing 10000000 bp from intervals
19:08:51.454 INFO VariantRecalibrator - Done initializing engine
19:08:51.454 INFO TrainingSet - Found same track: Known = false Training = true Truth = true Prior = Q15.0
19:08:51.465 INFO ProgressMeter - Starting traversal
19:08:51.465 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:08:51.528 INFO ProgressMeter - chr1:6212018 0.0 2791 2658095.2
19:08:51.528 INFO ProgressMeter - Traversal complete. Processed 2791 total variants in 0.0 minutes.
19:08:51.528 INFO VariantDataManager - AS_QD: mean = 20.88 standard deviation = 8.12
19:08:51.529 INFO VariantDataManager - AS_ReadPosRankSum: mean = -0.05 standard deviation = 0.74
19:08:51.529 INFO VariantDataManager - AS_MQ: mean = 59.82 standard deviation = 2.48
19:08:51.529 INFO VariantDataManager - AS_SOR: mean = 0.86 standard deviation = 0.67
19:08:51.530 INFO VariantDataManager - Annotation order is: [AS_QD, AS_ReadPosRankSum, AS_MQ, AS_SOR]
19:08:51.530 INFO VariantDataManager - Training with 2774 variants after standard deviation thresholding.
19:08:51.530 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:51.562 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:51.579 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.12046
19:08:51.595 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.09714
19:08:51.612 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.07781
19:08:51.629 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.05863
19:08:51.645 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01774
19:08:51.662 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00612
19:08:51.679 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00395
19:08:51.696 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00313
19:08:51.713 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00276
19:08:51.729 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00245
19:08:51.746 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00219
19:08:51.763 INFO VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00198
19:08:51.763 INFO VariantRecalibratorEngine - Convergence after 60 iterations!
19:08:51.764 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
19:08:51.773 INFO VariantDataManager - Selected worst 6 scoring variants --> variants with LOD <= -5.0000.
19:08:51.773 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:51.773 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:51.773 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
19:08:51.773 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
19:08:51.781 INFO TrancheManager - Finding 4 tranches for 2786 variants
19:08:51.783 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
19:08:51.783 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
19:08:51.783 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]
19:08:51.783 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
19:08:51.783 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 3; running score is 0.001
19:08:51.783 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]
19:08:51.783 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
19:08:51.784 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 28; running score is 0.010
19:08:51.784 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]
19:08:51.784 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
19:08:51.784 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 279; running score is 0.100
19:08:51.784 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]
19:08:51.784 INFO VariantRecalibrator - Writing out recalibration table...
19:08:51.801 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:08:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=954204160
19:08:51.805 INFO gatk - Initializing VQSR tests/resetting random number generator
19:08:51.815 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:51.815 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:08:51.815 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:08:51.815 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:08:51.815 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:08:51.815 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:08:51 PM UTC
19:08:51.815 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:51.815 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:51.815 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:08:51.815 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:08:51.815 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:08:51.815 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:08:51.815 INFO VariantRecalibrator - Deflater: IntelDeflater
19:08:51.815 INFO VariantRecalibrator - Inflater: IntelInflater
19:08:51.816 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:08:51.816 INFO VariantRecalibrator - Requester pays: disabled
19:08:51.816 INFO VariantRecalibrator - Initializing engine
19:08:51.817 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
19:08:51.818 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
19:08:51.819 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
19:08:51.821 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
19:08:51.823 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
19:08:51.823 INFO VariantRecalibrator - Done initializing engine
19:08:51.824 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
19:08:51.824 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
19:08:51.824 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
19:08:51.824 INFO ProgressMeter - Starting traversal
19:08:51.825 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:08:52.782 INFO ProgressMeter - 20:9944766 0.0 131821 8264639.5
19:08:52.783 INFO ProgressMeter - Traversal complete. Processed 131821 total variants in 0.0 minutes.
19:08:52.785 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
19:08:52.788 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
19:08:52.791 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
19:08:52.810 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
19:08:52.811 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
19:08:52.811 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:53.075 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:53.181 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.42302
19:08:53.288 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24203
19:08:53.398 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15214
19:08:53.510 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.22858
19:08:53.623 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07799
19:08:53.735 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04227
19:08:53.850 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00976
19:08:53.954 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03859
19:08:54.043 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.18953
19:08:54.132 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01049
19:08:54.203 INFO VariantRecalibratorEngine - Convergence after 54 iterations!
19:08:54.211 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
19:08:54.282 INFO VariantDataManager - Selected worst 474 scoring variants --> variants with LOD <= -5.0000.
19:08:54.283 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:54.284 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:54.285 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
19:08:54.286 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
19:08:54.472 INFO TrancheManager - Finding 12 tranches for 131821 variants
19:08:54.512 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
19:08:54.517 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
19:08:54.517 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]
19:08:54.517 INFO TrancheManager - TruthSensitivityTranche threshold 99.95 => selection metric threshold 0.000
19:08:54.523 INFO TrancheManager - Found tranche for 99.950: 0.000 threshold starting with variant 381; running score is 0.001
19:08:54.523 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]
19:08:54.523 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
19:08:54.528 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 747; running score is 0.001
19:08:54.528 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]
19:08:54.529 INFO TrancheManager - TruthSensitivityTranche threshold 99.80 => selection metric threshold 0.002
19:08:54.533 INFO TrancheManager - Found tranche for 99.800: 0.002 threshold starting with variant 1480; running score is 0.002
19:08:54.533 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]
19:08:54.533 INFO TrancheManager - TruthSensitivityTranche threshold 99.60 => selection metric threshold 0.004
19:08:54.537 INFO TrancheManager - Found tranche for 99.600: 0.004 threshold starting with variant 2377; running score is 0.004
19:08:54.538 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]
19:08:54.538 INFO TrancheManager - TruthSensitivityTranche threshold 99.50 => selection metric threshold 0.005
19:08:54.542 INFO TrancheManager - Found tranche for 99.500: 0.005 threshold starting with variant 3042; running score is 0.005
19:08:54.542 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]
19:08:54.542 INFO TrancheManager - TruthSensitivityTranche threshold 99.40 => selection metric threshold 0.006
19:08:54.546 INFO TrancheManager - Found tranche for 99.400: 0.006 threshold starting with variant 3577; running score is 0.006
19:08:54.546 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]
19:08:54.547 INFO TrancheManager - TruthSensitivityTranche threshold 99.30 => selection metric threshold 0.007
19:08:54.551 INFO TrancheManager - Found tranche for 99.300: 0.007 threshold starting with variant 4004; running score is 0.007
19:08:54.551 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]
19:08:54.551 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
19:08:54.555 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 5604; running score is 0.010
19:08:54.556 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]
19:08:54.556 INFO TrancheManager - TruthSensitivityTranche threshold 98.00 => selection metric threshold 0.020
19:08:54.560 INFO TrancheManager - Found tranche for 98.000: 0.020 threshold starting with variant 10673; running score is 0.020
19:08:54.560 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]
19:08:54.560 INFO TrancheManager - TruthSensitivityTranche threshold 97.00 => selection metric threshold 0.030
19:08:54.564 INFO TrancheManager - Found tranche for 97.000: 0.030 threshold starting with variant 16985; running score is 0.030
19:08:54.564 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]
19:08:54.564 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
19:08:54.568 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 63492; running score is 0.100
19:08:54.568 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]
19:08:54.568 INFO VariantRecalibrator - Writing out recalibration table...
19:08:54.886 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:08:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=954204160
19:08:54.907 INFO gatk - Initializing VQSR tests/resetting random number generator
19:08:54.919 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:54.919 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:08:54.919 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:08:54.919 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:08:54.920 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:08:54.920 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:08:54 PM UTC
19:08:54.920 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:54.920 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:54.920 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:08:54.920 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:08:54.920 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:08:54.920 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:08:54.920 INFO VariantRecalibrator - Deflater: IntelDeflater
19:08:54.920 INFO VariantRecalibrator - Inflater: IntelInflater
19:08:54.920 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:08:54.920 INFO VariantRecalibrator - Requester pays: disabled
19:08:54.920 INFO VariantRecalibrator - Initializing engine
19:08:54.921 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
19:08:54.938 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
19:08:54.977 INFO IntervalArgumentCollection - Processing 10000000 bp from intervals
19:08:54.991 INFO VariantRecalibrator - Done initializing engine
19:08:54.992 INFO TrainingSet - Found same track: Known = false Training = true Truth = true Prior = Q15.0
19:08:55.002 INFO ProgressMeter - Starting traversal
19:08:55.002 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:08:55.046 INFO ProgressMeter - chr1:6212018 0.0 2791 3805909.1
19:08:55.046 INFO ProgressMeter - Traversal complete. Processed 2791 total variants in 0.0 minutes.
19:08:55.046 INFO VariantDataManager - AS_QD: mean = 20.88 standard deviation = 8.12
19:08:55.046 INFO VariantDataManager - AS_ReadPosRankSum: mean = -0.05 standard deviation = 0.74
19:08:55.047 INFO VariantDataManager - AS_MQ: mean = 59.82 standard deviation = 2.48
19:08:55.047 INFO VariantDataManager - AS_SOR: mean = 0.86 standard deviation = 0.67
19:08:55.047 INFO VariantDataManager - Annotation order is: [AS_QD, AS_ReadPosRankSum, AS_MQ, AS_SOR]
19:08:55.047 INFO VariantDataManager - Training with 2774 variants after standard deviation thresholding.
19:08:55.048 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:55.080 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:55.097 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.12046
19:08:55.114 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.09714
19:08:55.131 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.07781
19:08:55.148 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.05863
19:08:55.164 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01774
19:08:55.181 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00612
19:08:55.198 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00395
19:08:55.215 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00313
19:08:55.232 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00276
19:08:55.249 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00245
19:08:55.266 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00219
19:08:55.286 INFO VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00198
19:08:55.286 INFO VariantRecalibratorEngine - Convergence after 60 iterations!
19:08:55.288 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
19:08:55.297 INFO VariantDataManager - Selected worst 6 scoring variants --> variants with LOD <= -5.0000.
19:08:55.297 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:55.297 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:55.297 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
19:08:55.297 INFO VariantRecalibratorEngine - Evaluating full set of 2786 variants...
19:08:55.305 INFO TrancheManager - Finding 12 tranches for 2786 variants
19:08:55.305 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
19:08:55.305 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
19:08:55.306 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]
19:08:55.306 INFO TrancheManager - TruthSensitivityTranche threshold 99.95 => selection metric threshold 0.000
19:08:55.306 INFO TrancheManager - Found tranche for 99.950: 0.000 threshold starting with variant 2; running score is 0.001
19:08:55.306 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]
19:08:55.306 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
19:08:55.306 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 3; running score is 0.001
19:08:55.306 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]
19:08:55.306 INFO TrancheManager - TruthSensitivityTranche threshold 99.80 => selection metric threshold 0.002
19:08:55.306 INFO TrancheManager - Found tranche for 99.800: 0.002 threshold starting with variant 6; running score is 0.002
19:08:55.306 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]
19:08:55.307 INFO TrancheManager - TruthSensitivityTranche threshold 99.60 => selection metric threshold 0.004
19:08:55.307 INFO TrancheManager - Found tranche for 99.600: 0.004 threshold starting with variant 12; running score is 0.004
19:08:55.307 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]
19:08:55.307 INFO TrancheManager - TruthSensitivityTranche threshold 99.50 => selection metric threshold 0.005
19:08:55.307 INFO TrancheManager - Found tranche for 99.500: 0.005 threshold starting with variant 14; running score is 0.005
19:08:55.307 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]
19:08:55.307 INFO TrancheManager - TruthSensitivityTranche threshold 99.40 => selection metric threshold 0.006
19:08:55.307 INFO TrancheManager - Found tranche for 99.400: 0.006 threshold starting with variant 17; running score is 0.006
19:08:55.307 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]
19:08:55.307 INFO TrancheManager - TruthSensitivityTranche threshold 99.30 => selection metric threshold 0.007
19:08:55.308 INFO TrancheManager - Found tranche for 99.300: 0.007 threshold starting with variant 20; running score is 0.007
19:08:55.308 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]
19:08:55.308 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
19:08:55.308 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 28; running score is 0.010
19:08:55.308 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]
19:08:55.308 INFO TrancheManager - TruthSensitivityTranche threshold 98.00 => selection metric threshold 0.020
19:08:55.308 INFO TrancheManager - Found tranche for 98.000: 0.020 threshold starting with variant 56; running score is 0.020
19:08:55.309 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]
19:08:55.309 INFO TrancheManager - TruthSensitivityTranche threshold 97.00 => selection metric threshold 0.030
19:08:55.309 INFO TrancheManager - Found tranche for 97.000: 0.030 threshold starting with variant 84; running score is 0.030
19:08:55.309 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]
19:08:55.309 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
19:08:55.310 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 279; running score is 0.100
19:08:55.310 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]
19:08:55.310 INFO VariantRecalibrator - Writing out recalibration table...
19:08:55.328 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:08:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=954204160
19:08:55.331 INFO gatk - Initializing VQSR tests/resetting random number generator
[May 19, 2025 at 7:08:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=954204160
19:08:57.728 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:57.728 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:08:57.728 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:08:57.728 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:08:57.728 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:08:57.729 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:08:57 PM UTC
19:08:57.729 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:57.729 INFO VariantRecalibrator - ------------------------------------------------------------
19:08:57.729 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:08:57.729 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:08:57.729 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:08:57.729 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:08:57.729 INFO VariantRecalibrator - Deflater: IntelDeflater
19:08:57.729 INFO VariantRecalibrator - Inflater: IntelInflater
19:08:57.729 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:08:57.729 INFO VariantRecalibrator - Requester pays: disabled
19:08:57.729 INFO VariantRecalibrator - Initializing engine
19:08:57.730 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
19:08:57.732 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
19:08:57.733 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
19:08:57.734 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
19:08:57.736 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
19:08:57.747 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
19:08:57.748 INFO VariantRecalibrator - Done initializing engine
19:08:57.748 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
19:08:57.748 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
19:08:57.748 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
19:08:57.751 INFO ProgressMeter - Starting traversal
19:08:57.751 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:08:58.727 INFO ProgressMeter - 20:9938789 0.0 134919 8294200.8
19:08:58.727 INFO ProgressMeter - Traversal complete. Processed 134919 total variants in 0.0 minutes.
19:08:58.730 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
19:08:58.733 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
19:08:58.736 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
19:08:58.758 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
19:08:58.760 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
19:08:58.760 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:58.972 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:59.053 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.13181
19:08:59.135 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.46782
19:08:59.222 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 9.04961
19:08:59.290 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.04477
19:08:59.357 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01711
19:08:59.424 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.02053
19:08:59.491 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.01194
19:08:59.558 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01038
19:08:59.625 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.06192
19:08:59.693 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01281
19:08:59.763 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00457
19:08:59.791 INFO VariantRecalibratorEngine - Convergence after 57 iterations!
19:08:59.796 INFO VariantRecalibratorEngine - Evaluating full set of 134603 variants...
19:08:59.894 INFO VariantDataManager - Selected worst 754 scoring variants --> variants with LOD <= -5.0000.
19:08:59.894 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:08:59.897 INFO VariantRecalibratorEngine - Finished iteration 0.
19:08:59.898 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.05287
19:08:59.899 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.02030
19:08:59.900 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.00986
19:08:59.901 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.00749
19:08:59.902 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.00850
19:08:59.904 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.01430
19:08:59.905 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02541
19:08:59.906 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.02173
19:08:59.907 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.01024
19:08:59.908 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00479
19:08:59.909 INFO VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00245
19:08:59.910 INFO VariantRecalibratorEngine - Convergence after 57 iterations!
19:08:59.912 INFO VariantRecalibratorEngine - Evaluating full set of 134603 variants...
19:09:00.082 INFO TrancheManager - Finding 4 tranches for 134603 variants
19:09:00.117 INFO TrancheManager - TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
19:09:00.121 INFO TrancheManager - Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000
19:09:00.122 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]
19:09:00.122 INFO TrancheManager - TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
19:09:00.126 INFO TrancheManager - Found tranche for 99.900: 0.001 threshold starting with variant 649; running score is 0.001
19:09:00.126 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]
19:09:00.126 INFO TrancheManager - TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
19:09:00.130 INFO TrancheManager - Found tranche for 99.000: 0.010 threshold starting with variant 7924; running score is 0.010
19:09:00.130 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]
19:09:00.130 INFO TrancheManager - TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
19:09:00.134 INFO TrancheManager - Found tranche for 90.000: 0.100 threshold starting with variant 52632; running score is 0.100
19:09:00.134 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]
19:09:00.135 INFO VariantRecalibrator - Writing out recalibration table...
19:09:00.441 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:09:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=954204160
19:09:00.443 INFO gatk - Initializing VQSR tests/resetting random number generator
19:09:00.450 INFO VariantRecalibrator - ------------------------------------------------------------
19:09:00.450 INFO VariantRecalibrator - org.broadinstitute.hellbender.tools.walkers.vqsr vUnavailable
19:09:00.450 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:00.450 INFO VariantRecalibrator - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
19:09:00.451 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:09:00.451 INFO VariantRecalibrator - Start Date/Time: May 19, 2025 at 7:09:00 PM UTC
19:09:00.451 INFO VariantRecalibrator - ------------------------------------------------------------
19:09:00.451 INFO VariantRecalibrator - ------------------------------------------------------------
19:09:00.451 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:00.451 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:00.451 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:00.451 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:00.451 INFO VariantRecalibrator - Deflater: IntelDeflater
19:09:00.451 INFO VariantRecalibrator - Inflater: IntelInflater
19:09:00.451 INFO VariantRecalibrator - GCS max retries/reopens: 20
19:09:00.451 INFO VariantRecalibrator - Requester pays: disabled
19:09:00.451 INFO VariantRecalibrator - Initializing engine
19:09:00.452 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
19:09:00.455 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
19:09:00.457 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
19:09:00.458 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
19:09:00.461 INFO IntervalArgumentCollection - Processing 9000001 bp from intervals
19:09:00.462 INFO VariantRecalibrator - Done initializing engine
19:09:00.462 INFO TrainingSet - Found known track: Known = true Training = false Truth = false Prior = Q10.0
19:09:00.462 INFO TrainingSet - Found truth_training1 track: Known = false Training = true Truth = true Prior = Q15.0
19:09:00.462 INFO TrainingSet - Found truth_training2 track: Known = false Training = true Truth = true Prior = Q12.0
19:09:00.463 INFO ProgressMeter - Starting traversal
19:09:00.463 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:09:01.426 INFO ProgressMeter - 20:9944766 0.0 131821 8213146.4
19:09:01.426 INFO ProgressMeter - Traversal complete. Processed 131821 total variants in 0.0 minutes.
19:09:01.428 INFO VariantDataManager - QD: mean = 16.58 standard deviation = 5.43
19:09:01.432 INFO VariantDataManager - HaplotypeScore: mean = 0.27 standard deviation = 0.27
19:09:01.435 INFO VariantDataManager - HRun: mean = 0.59 standard deviation = 0.99
19:09:01.456 INFO VariantDataManager - Annotation order is: [QD, HRun, HaplotypeScore]
19:09:01.457 INFO VariantDataManager - Training with 18642 variants after standard deviation thresholding.
19:09:01.457 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:09:01.726 INFO VariantRecalibratorEngine - Finished iteration 0.
19:09:01.834 INFO VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.42302
19:09:01.944 INFO VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24203
19:09:02.058 INFO VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15214
19:09:02.167 INFO VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.22858
19:09:02.285 INFO VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07799
19:09:02.375 INFO VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04227
19:09:02.468 INFO VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00976
19:09:02.558 INFO VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03859
19:09:02.647 INFO VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.18953
19:09:02.737 INFO VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.01049
19:09:02.808 INFO VariantRecalibratorEngine - Convergence after 54 iterations!
19:09:02.815 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
19:09:02.882 INFO VariantDataManager - Selected worst 474 scoring variants --> variants with LOD <= -5.0000.
19:09:02.883 INFO GaussianMixtureModel - Initializing model with 100 k-means iterations...
19:09:02.884 INFO VariantRecalibratorEngine - Finished iteration 0.
19:09:02.884 INFO VariantRecalibratorEngine - Convergence after 3 iterations!
19:09:02.886 INFO VariantRecalibratorEngine - Evaluating full set of 131821 variants...
19:09:03.074 INFO TrancheManager - Finding 12 tranches for 131821 variants
19:09:03.109 INFO TrancheManager - VQSLODTranche threshold 10.00 => selection metric threshold 0.900
19:09:03.117 INFO TrancheManager - Found tranche for 10.000: 0.900 threshold starting with variant 97819; running score is 0.262
19:09:03.118 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=10.0000 known=(29048 @ 2.5026) novel=(4954 @ 2.3633) truthSites(18665 accessible, 13780 called), name=anonymous]
19:09:03.118 INFO TrancheManager - VQSLODTranche threshold 8.00 => selection metric threshold 0.920
19:09:03.122 INFO TrancheManager - Found tranche for 8.000: 0.920 threshold starting with variant 68875; running score is 0.114
19:09:03.123 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=8.0000 known=(44004 @ 2.4829) novel=(18942 @ 2.4147) truthSites(18665 accessible, 16543 called), name=anonymous]
19:09:03.123 INFO TrancheManager - VQSLODTranche threshold 6.00 => selection metric threshold 0.940
19:09:03.131 INFO TrancheManager - Found tranche for 6.000: 0.940 threshold starting with variant 34094; running score is 0.052
19:09:03.131 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=6.0000 known=(52474 @ 2.4242) novel=(45253 @ 2.3994) truthSites(18665 accessible, 17701 called), name=anonymous]
19:09:03.131 INFO TrancheManager - VQSLODTranche threshold 4.00 => selection metric threshold 0.960
19:09:03.138 INFO TrancheManager - Found tranche for 4.000: 0.960 threshold starting with variant 12275; running score is 0.023
19:09:03.138 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=4.0000 known=(56181 @ 2.3913) novel=(63365 @ 2.3212) truthSites(18665 accessible, 18243 called), name=anonymous]
19:09:03.138 INFO TrancheManager - VQSLODTranche threshold 2.00 => selection metric threshold 0.980
19:09:03.145 INFO TrancheManager - Found tranche for 2.000: 0.980 threshold starting with variant 4952; running score is 0.009
19:09:03.145 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=2.0000 known=(57758 @ 2.3573) novel=(69111 @ 2.2722) truthSites(18665 accessible, 18502 called), name=anonymous]
19:09:03.145 INFO TrancheManager - VQSLODTranche threshold 0.00 => selection metric threshold 1.000
19:09:03.150 INFO TrancheManager - Found tranche for 0.000: 1.000 threshold starting with variant 2260; running score is 0.004
19:09:03.150 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=0.0000 known=(58579 @ 2.3306) novel=(70982 @ 2.2511) truthSites(18665 accessible, 18598 called), name=anonymous]
19:09:03.150 INFO TrancheManager - VQSLODTranche threshold -2.00 => selection metric threshold 1.020
19:09:03.155 INFO TrancheManager - Found tranche for -2.000: 1.020 threshold starting with variant 1099; running score is 0.001
19:09:03.155 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-2.0000 known=(59019 @ 2.3111) novel=(71703 @ 2.2372) truthSites(18665 accessible, 18640 called), name=anonymous]
19:09:03.155 INFO TrancheManager - VQSLODTranche threshold -4.00 => selection metric threshold 1.040
19:09:03.160 INFO TrancheManager - Found tranche for -4.000: 1.040 threshold starting with variant 606; running score is 0.001
19:09:03.160 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-4.0000 known=(59205 @ 2.3054) novel=(72010 @ 2.2272) truthSites(18665 accessible, 18648 called), name=anonymous]
19:09:03.160 INFO TrancheManager - VQSLODTranche threshold -6.00 => selection metric threshold 1.060
19:09:03.165 INFO TrancheManager - Found tranche for -6.000: 1.060 threshold starting with variant 429; running score is 0.001
19:09:03.165 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-6.0000 known=(59292 @ 2.3026) novel=(72100 @ 2.2261) truthSites(18665 accessible, 18653 called), name=anonymous]
19:09:03.165 INFO TrancheManager - VQSLODTranche threshold -8.00 => selection metric threshold 1.080
19:09:03.169 INFO TrancheManager - Found tranche for -8.000: 1.080 threshold starting with variant 314; running score is 0.000
19:09:03.169 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-8.0000 known=(59355 @ 2.3009) novel=(72152 @ 2.2247) truthSites(18665 accessible, 18657 called), name=anonymous]
19:09:03.169 INFO TrancheManager - VQSLODTranche threshold -10.00 => selection metric threshold 1.100
19:09:03.174 INFO TrancheManager - Found tranche for -10.000: 1.100 threshold starting with variant 264; running score is 0.000
19:09:03.174 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-10.0000 known=(59372 @ 2.3008) novel=(72185 @ 2.2246) truthSites(18665 accessible, 18658 called), name=anonymous]
19:09:03.174 INFO TrancheManager - VQSLODTranche threshold -12.00 => selection metric threshold 1.120
19:09:03.178 INFO TrancheManager - Found tranche for -12.000: 1.120 threshold starting with variant 211; running score is 0.000
19:09:03.178 INFO TrancheManager - VQSLODTranche is Tranche minVQSLod=-12.0000 known=(59394 @ 2.3004) novel=(72216 @ 2.2244) truthSites(18665 accessible, 18659 called), name=anonymous]
19:09:03.178 INFO VariantRecalibrator - Writing out recalibration table...
19:09:03.484 INFO VariantRecalibrator - Tranches plot will not be generated since we are running in scattered mode
19:09:03.487 INFO VariantRecalibrator - Shutting down engine
[May 19, 2025 at 7:09:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=954204160
[May 19, 2025 at 7:10:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1497366528