To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

an error about doing Count covariates

I am running the Quality score recalibration and got an version error like this:

`java -Xmx4g -jar ~/GenomeAnalysisTK-2.1-3/GenomeAnalysisTK.jar -l INFO -R hg19.fa --DBSNP snp137.txt -I sdD1a_bam.marked.realigned.fixed.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile sdD1a.recal_data.csv &
[11] 9980
[c@scigc-vm-10 shones]$ ##### ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 2.1-3-g8892c10):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0
ERROR ------------------------------------------------------------------------------------------`

Is there a solution for that?
Thanks.

Tagged:

Answers

Sign In or Register to comment.