Question: Gatk Error Argument With Name 'T' Isn'T Defined
4.2 years ago by
Erica Westerman • 10
Erica Westerman • 10 wrote:
Aloha. I am using GATK in Galaxy for the first time, on a local Galaxy server, and when I try to run Count Covariates I get the error: ERROR stack trace org.broadinstitute.sting.commandline.InvalidArgumentException: Argument with name 'T' isn't defined. at org.broadinstitute.s I have looked at the GATK Count Covariates command line, and it looks to me like the argument with name 'T' is not a place where I need to input a file, but is where the Count Covariates software information goes. I get this same error when trying to run Realigner Target Creator. I wondered if this might be something that could be simply fixed by reinstalling the wrappers for GATK, or something along those lines? Thank you!
ADD COMMENT • link •