Thanks for the suggestin Linda...

i removed the line
 -et "NO_ET" ##ET no phone home

Now i am not  getting the Error as get key to run the GATK..
But i am getting error as the fasta file is not found..

even in backend i found the command as mentioned below
in the reference file section "-R " there is no link for the fasta file..
Please give the suggestion.. i mentioned many time this Error but i am not getting any reply..


python /illumina/data/galaxy/galaxy-dist/tools/gatk/gatk_wrapper.py    --max_jvm_heap_fraction "1"    --stdout "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_843.dat"        -d "-I" "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_539.dat" "bam" "gatk_input_0"            -d "" "/illumina/data/galaxy/galaxy-dist/database/files/_metadata_files/000/metadata_30.dat" "bam_index" "gatk_input_0"     -p 'java      -jar "/illumina/data/galaxy/galaxy-dist/tool-data/shared/jars/gatk/GenomeAnalysisTK.jar"     -T "UnifiedGenotyper"     --num_threads 4      --out "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_841.dat"     --metrics_file "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_842.dat"             -R ""     --genotype_likelihoods_model "BOTH"     --standard_min_confidence_threshold_for_calling "30.0"     --standard_min_confidence_threshold_for_emitting "30.0"    '


Thanks
Sridhar


On Tue, Jun 11, 2013 at 1:01 PM, sridhar srinivasan <sridhar2bioinfo@gmail.com> wrote:
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 <lcham@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.



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 <sridhar2bioinfo@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-bounces@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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