Hi Sridhar,

About the error, you need to request a key from GATK

http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
See under "How to obtain and use a GATK key"

Or by pass it by removing the -et "NO_ET" line from the xml files.





From:   sridhar srinivasan <sridhar2bioi...@gmail.com>
To:     Galaxy Dev <galaxy-dev@lists.bx.psu.edu>
Date:   06/06/2013 06:30 AM
Subject:        [galaxy-dev] GATK
Sent by:        galaxy-dev-boun...@lists.bx.psu.edu



Dear Developers,

I am running GATK for first time. In galaxy i use Unified Genotyper. I am
getting error as below mentioned.

##### ERROR
------------------------------------------------------------------------------------------


##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
##### 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: Running with the -et NO_ET or -et STDOUT option
requires a GATK Key file. Please see
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
 for more information and instructions on how to obtain a key.

##### ERROR
------------------------------------------------------------------------------------------

also suggest me about the Rod file for dbSNP.

Thanks

Sridhar___________________________________________________________
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