Do you have Cloudman admin access on this instance? The first thing I'd check would be http://<your_instance>/cloud to verify that your instance has free disk space and to look for any errors in the log. Then, check out the admin service list (http://<your_instance>/cloud/admin) to see if there are any service issues. Next to the SGE service, you should see a 'qstat' link that'll show you the status of any jobs submitted to the cluster. If you're not running any extra worker nodes, check this page to verify that the master is set to run jobs. If you look through this stuff and nothing looks obvious, feel free to ping me off list and I can try to take a look with you. -Dannon On Fri, Apr 25, 2014 at 2:18 AM, Alessia Deglincerti < adeglincer@mail.rockefeller.edu> wrote:

Hey Dannon,

I am using Galaxy (Cloudman) to analyze RNA seq data. I have a bunch of datasets that I ran TopHat on. I am now trying to run Cufflinks etc. I used the same data and workflow yesterday to run Cufflinks etc and that worked fine. I used my own reference annotation (Homo sapiens hg38) that I imported from UCSC but I wanted to compare to some older data I have and so now I trying to run it on hg17. I also have some other datasets in the queue. All my jobs are gray and have been waiting to ran for the past 24+ hours. I am seeing the error as I am waiting for my jobs to run, I get a notification at the top of my queue/history saying that there was a problem getting updates and to contact a site administrator if the problem persists (I've seen the notification a few times) and when I click the "details" link in the notification it prompts me with the details pasted below.

I am using all of the default options for my jobs and the same workflow has been working fine for me in the past on the same datasets.

Thanks for any help you can give me!

Alessia

On Apr 24, 2014, at 10:24 PM, Dannon Baker <dannon.baker@gmail.com> wrote:

Hey Alessia,

I'd love to help, but I need a little more context here. Where are you seeing this error, what exactly are you doing when it appears, and can you tell me a little bit more about the Galaxy configuration you're working with?

-Dannon

On Thu, Apr 24, 2014 at 8:37 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

...

Posting to the galaxy-dev@bx.psu.edu mailing list. https://wiki.galaxyproject.org/MailingLists

My instance of Galaxy seems to be stuck (same place since last night) and I have received the error message several times now.

Pasting the error message below:

*Details*

user

username

adeglincer

quota_percent

68

total_disk_usage

184947273683

nice_total_disk_usage

172.2 GB

email

xxx

is_admin

false

tags_used

model_class

User

id

xxx

source

HDACollection(xxx)

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

Date

Thu, 24 Apr 2014 20:51:39 GMT

cache-control

max-age=0,no-cache,no-store

Server

nginx/1.4.7

Connection

keep-alive

Transfer-Encoding

chunked

Content-Type

application/json

options

data

parse

true

emulateHTTP

false

emulateJSON

false

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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/