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VQSR error: NaN LOD value assigned

songsysongsy University of MichiganPosts: 3Member
edited February 26 in Ask the GATK team
INFO  17:05:50,124 GenomeAnalysisEngine - Preparing for traversal 
INFO 17:05:50,144 GenomeAnalysisEngine - Done preparing for traversal
INFO 17:05:50,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 17:05:50,145 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 17:05:50,166 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0
INFO 17:05:50,166 TrainingSet - Found omni track: Known = false Training = true Truth = false Prior = Q12.0
INFO 17:05:50,167 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q6.0
INFO 17:06:20,149 ProgressMeter - 1:216404576 2.04e+06 30.0 s 14.0 s 7.0% 7.2 m 6.7 m
INFO 17:06:50,151 ProgressMeter - 2:223579089 4.70e+06 60.0 s 12.0 s 15.2% 6.6 m 5.6 m
INFO 17:07:20,159 ProgressMeter - 4:33091662 7.43e+06 90.0 s 12.0 s 23.3% 6.4 m 4.9 m
INFO 17:07:50,161 ProgressMeter - 5:92527959 1.00e+07 120.0 s 11.0 s 31.4% 6.4 m 4.4 m
INFO 17:08:20,162 ProgressMeter - 7:1649969 1.30e+07 2.5 m 11.0 s 39.8% 6.3 m 3.8 m
INFO 17:08:50,168 ProgressMeter - 8:106975025 1.58e+07 3.0 m 11.0 s 48.4% 6.2 m 3.2 m
INFO 17:09:20,169 ProgressMeter - 10:101433561 1.87e+07 3.5 m 11.0 s 57.4% 6.1 m 2.6 m
INFO 17:09:50,170 ProgressMeter - 12:99334147 2.16e+07 4.0 m 11.0 s 66.1% 6.1 m 2.1 m
INFO 17:10:20,171 ProgressMeter - 15:30577012 2.41e+07 4.5 m 11.0 s 75.4% 6.0 m 88.0 s
INFO 17:10:52,409 ProgressMeter - 18:8763648 2.68e+07 5.0 m 11.0 s 83.5% 6.0 m 59.0 s
INFO 17:11:22,410 ProgressMeter - 22:31598896 2.97e+07 5.5 m 11.0 s 92.2% 6.0 m 27.0 s
INFO 17:11:33,135 VariantDataManager - QD: mean = 17.48 standard deviation = 9.03
INFO 17:11:33,516 VariantDataManager - HaplotypeScore: mean = 3.03 standard deviation = 2.62
INFO 17:11:33,882 VariantDataManager - MQ: mean = 52.40 standard deviation = 2.98
INFO 17:11:34,253 VariantDataManager - MQRankSum: mean = 0.31 standard deviation = 1.02
INFO 17:11:37,973 VariantDataManager - Training with 1024360 variants after standard deviation thresholding.
INFO 17:11:37,977 GaussianMixtureModel - Initializing model with 30 k-means iterations...
INFO 17:11:53,065 ProgressMeter - GL000202.1:10465 3.08e+07 6.0 m 11.0 s 99.8% 6.0 m 0.0 s
INFO 17:12:09,041 VariantRecalibratorEngine - Finished iteration 0.
INFO 17:12:23,066 ProgressMeter - GL000202.1:10465 3.08e+07 6.5 m 12.0 s 99.8% 6.5 m 0.0 s
INFO 17:12:30,492 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.08178
INFO 17:12:51,054 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.05869
INFO 17:12:53,072 ProgressMeter - GL000202.1:10465 3.08e+07 7.0 m 13.0 s 99.8% 7.0 m 0.0 s
INFO 17:13:11,207 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.15237
INFO 17:13:23,073 ProgressMeter - GL000202.1:10465 3.08e+07 7.5 m 14.0 s 99.8% 7.5 m 0.0 s
INFO 17:13:31,503 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.13505
INFO 17:13:51,768 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.05729
INFO 17:13:53,080 ProgressMeter - GL000202.1:10465 3.08e+07 8.0 m 15.0 s 99.8% 8.0 m 0.0 s
INFO 17:14:11,372 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.02607
INFO 17:14:23,081 ProgressMeter - GL000202.1:10465 3.08e+07 8.5 m 16.0 s 99.8% 8.5 m 0.0 s
INFO 17:14:24,730 VariantRecalibratorEngine - Convergence after 33 iterations!
INFO 17:14:27,037 VariantRecalibratorEngine - Evaluating full set of 3860460 variants...
INFO 17:14:51,111 VariantDataManager - Found 0 variants overlapping bad sites training tracks.
INFO 17:14:55,071 VariantDataManager - Additionally training with worst 1000 scoring variants --> 1000 variants with LOD <= -30.5662.
INFO 17:14:55,071 GaussianMixtureModel - Initializing model with 30 k-means iterations...
INFO 17:14:55,082 VariantRecalibratorEngine - Finished iteration 0.
INFO 17:14:55,095 VariantRecalibratorEngine - Convergence after 4 iterations!
INFO 17:14:55,096 VariantRecalibratorEngine - Evaluating full set of 3860460 variants...
INFO 17:15:02,071 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.7-2-g6bda569):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --numBad 3000, for example).
##### ERROR ------------------------------------------------------------------------------------------

My command is :

java -jar -Xmx4g GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar -T VariantRecalibrator -R human_g1k_v37.fasta -input NA12878_snp.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_132.b37.vcf -an QD -an HaplotypeScore -an MQ -an MQRankSum --maxGaussians 4 -mode SNP -recalFile NA12878_recal.vcf -tranchesFile NA12878_tranches -rscriptFile NA12878.plots.R

Before I didn't use -maxGaussians 4, once an error suggested this, I tried but still got this error message...And I think that numBad is already deprecated. I don't understand why this error will happen. I'm doing GATK unifiedgenotyper on 1000Genomes high coverage bam file and then use VQSR to filter the snp.

Post edited by Geraldine_VdAuwera on
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