Hello,
The error is about 'no sequences being available for the database specified'. But no database is assigned to the GTF file because you are using a custom reference genome. The solution: set the reference database to be used from the history, then choose the .fasta version of your custom reference genome dataset.
If you were in the UI, the tool form option would be "Choose the source for the reference list:". You have it set now to be "Locally cashed" which interprets the database (dbkey) assignment of the input file and uses data native to the instance. Instead, you want this set to "History" and to then select the dataset that is the custom reference genome.
Hopefully this helps!
Jen Galaxy team
ps. Please note that this list will fully phase out very soon. New questions should be directed to the Galaxy Biostar forum. See this wiki for how to get started: https://wiki.galaxyproject.org/Support#Biostar
On 5/16/14 2:10 AM, Antoine Buetti-Dinh wrote:
Hi,
sorry to bother but now it's the 3rd time I get a message saying that if the problem persists I should contact the galaxy staff.
It occurs while running cuffcompare of total RNA to a genomic reference that I uploaded myself (Sulfolobus acidocaldarius). It's about MPI processes terminated incorrectly if I understood it correctly.
Just to let you know...
These are the details of the generated error:
user username twincacca quota_percent 32 total_disk_usage 86918246471 nice_total_disk_usage 80.9 GB email antoine.buetti@lnu.se is_admin false tags_used model_class User id 3e934cb0877d45db source HDACollection(8fb8cc6fa23b1dbe,99) xhr readyState 4 responseText {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0} responseJSON err_msg Uncaught exception in exposed API method: err_code 0 status 500 statusText Internal Server Error responseHeaders Server nginx/1.4.7 Date Fri, 16 May 2014 08:58:57 GMT Content-Type application/json Transfer-Encoding chunked Connection keep-alive Cache-Control max-age=0,no-cache,no-store options data parse true emulateHTTP false emulateJSON false ---------------------------------------------------------------END
The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/
Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar.
For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: