Hi Sridhar,

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

http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-... 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 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-... 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" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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-... 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 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*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-... *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" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/