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 [email protected]
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
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For discussion of local Galaxy instances and the Galaxy
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--
Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
