Hello Linda,
Thanks for your suggestions.

i removed the line from xml file but now i am getting different error.

##### 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: The fasta file you specified
(/tmp/tmp-gatk-sPZtN_) does not exist.
##### ERROR 
------------------------------------------------------------------------------------------

I mentioned the path  for human genome fasta file in .loc file , but
again i am getting same error.

I am using GATK latest (GenomeAnalysisTK-2.5-2-gf57256b) version.


your suggestions are very much appericiated..

Thanks
Sridhar





On Thu, Jun 6, 2013 at 5:23 PM, Linda Cham <lc...@us.ibm.com> wrote:

> 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.
>
>
>
> [image: Inactive hide details for sridhar srinivasan ---06/06/2013
> 06:30:48 AM---Dear Developers, I am running GATK for first time. In]sridhar
> srinivasan ---06/06/2013 06:30:48 AM---Dear Developers, I am running GATK
> for first time. In galaxy i use Unified Genotyper. I am
>
> 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*<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
> *<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___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>
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>

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