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
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.