Question: Cufflinks error: Uncaught exception in exposed API method
0
gravatar for n.ho
3.6 years ago by
n.ho0
United Kingdom
n.ho0 wrote:

Hi Galaxy Team

I've run into an error with my RNA-Seq analysis on usegalaxy.org 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?

Details
user    
username    n-ho
quota_percent    14
total_disk_usage    38805145805
nice_total_disk_usage    36.1 GB
email    n.ho@imperial.ac.uk
is_admin    false
tags_used    
model_class    User
id    e106ea66b78d4d17
source    HDACollection(21e2f44b7b2f6cd2,62)
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    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
options    
data    
parse    true
emulateHTTP    false
emulateJSON    false


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

Cheers,
Nick


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
1
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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