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 <
sridhar2bioi...@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 <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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