Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

Regards
GATK Staff

Warning message from VariantDataManager

helenehelene LAMember

Hello,

I notice the following warning messages during the first step of VQSR:

------------------------------------------------------------------------------------------
Done. There were 3 WARN messages, the first 3 are repeated below.
WARN  16:10:55,436 VariantDataManager - WARNING: Very large training set detected. Downsampling to 2500000 training variants. 
WARN  16:40:01,432 RScriptExecutor - RScript exited with 127. Run with -l DEBUG for more info. 
WARN  16:40:01,449 RScriptExecutor - RScript exited with 127. Run with -l DEBUG for more info. 

I know that the latter two is probably due to me not having the required R libraries set up, but what about the first warning on large training set please? My code is as the following and I'm using GATK 3.6:

 java -Xmx45g -jar $GATK -T VariantRecalibrator -R $REF -input ./INDIVIDUAL.raw.snps.indels.combined.vcf \
 -recalFile ./INDIVIDUAL.snp.recal \
 -tranchesFile ./INDIVIDUAL.snp.tranches \
 -rscriptFile ./INDIVIDUAL.snp.recalibrate_SNP_plots.R \
 -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /gatkRefDir/hapmap_3.3.hg19.sites.vcf \
 -resource:omni,known=false,training=true,truth=true,prior=12.0 /gatkRefDir/1000G_omni2.5.hg19.sites.vcf \
 -resource:1000G,known=false,training=true,truth=false,prior=10.0 /gatkRefDir/1000G_phase1.snps.high_confidence.hg19.sites.vcf \
 -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /gatkRefDir/dbsnp_138.hg19.vcf \
 -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP \
 -mode SNP 

Thanks a lot.

Helene

Tagged:

Best Answers

Answers

Sign In or Register to comment.