cuffcompare MPI error

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cuffcompare MPI error

Antoine Buetti-Dinh

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    [hidden email]
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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Re: cuffcompare MPI error

Jen Hillman-Jackson
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    [hidden email]
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:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
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/
Jennifer Hillman-Jackson
http://galaxyproject.org
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