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
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
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
xxx
is_admin
false
tags_used
model_classUser
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
parsetrue
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/
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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/
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
xxx
is_admin
false
tags_used
model_classUser
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
parsetrue
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/
galaxy-dev@lists.galaxyproject.org
-
Alessia Deglincerti -
Dannon Baker -
Jennifer Jackson