Question: Cufflinks error: Uncaught exception in exposed API method
gravatar for n.ho
3.6 years ago by
United Kingdom
n.ho0 wrote:

Hi Galaxy Team

I've run into an error with my RNA-Seq analysis on and would appreciate some feedback/advice.

I'm running Cufflinks on my TopHat accepted hits. I'm using a reference annotation file (a .gtf file that I previously ran through gffread to make sure that it's in an acceptable format) and with default parameters. After a few hours of the Cufflinks task queueing, an error message is thrown, however the task itself stays queued and 'grey'. Should I keep the task queueing/running or was there something I did incorrectly?

username    n-ho
quota_percent    14
total_disk_usage    38805145805
nice_total_disk_usage    36.1 GB
is_admin    false
model_class    User
id    e106ea66b78d4d17
source    HDACollection(21e2f44b7b2f6cd2,62)
readyState    4
responseText    {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
err_msg    Uncaught exception in exposed API method:
err_code    0
status    500
statusText    Internal Server Error
Server    nginx/1.4.7
Date    Tue, 10 Jun 2014 00:29:05 GMT
Content-Type    application/json
Transfer-Encoding    chunked
Connection    keep-alive
Cache-Control    max-age=0,no-cache,no-store
parse    true
emulateHTTP    false
emulateJSON    false

Let me know if I can provide more info and thanks in advance.


Nicholas Ho
Department of Life Sciences
Imperial College London
London, UK

api software error galaxy • 1.3k views
ADD COMMENTlink modified 3.6 years ago by Dannon Baker3.7k • written 3.6 years ago by n.ho0

We're taking a look at what may have caused the error you're seeing, but it shouldn't actually be related to your cufflinks job -- leave that in the state it's in and it should make it through the queue like normal.

ADD REPLYlink written 3.6 years ago by Dannon Baker3.7k
gravatar for Dannon Baker
3.6 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

Short answer is that this is an error on our side that shouldn't affect anything.  We'll get the bug fixed, but for now I think you should be able to simply refresh the browser window and continue using galaxy like normal.  There's currently a bit of a wait in the queue, but that job should run just fine.

ADD COMMENTlink written 3.6 years ago by Dannon Baker3.7k

Great, thanks!

ADD REPLYlink written 3.6 years ago by n.ho0
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