I'v run into this same issue again (just with some other Data Library
datasets). This time, there are a few users involved with quite a few
"stuck" jobs. Does anyone have any advice on pushing these jobs
through? Maybe even a pointer to the relevant code? I'm running
latest_2014.08.11. Thanks in advance.
Lance
Lance Parsons wrote:
Thanks, that was the first thing I checked. However, restarting the
handler didn't help. Downloading the offending data and re-uploading
as a new data set and then rerunning using the new dataset as input
did work. Also, all other jobs continued to run fine.
Lance
Kandalaft, Iyad wrote:
I’ve had jobs get stuck in the new state when one of the handler
servers crashes. If you have dedicated handlers, check to make sure
they are still running.
Restart the handler to see if the jobs get resumed automatically.
*Iyad Kandalaft*
*From:*galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Aaron Petkau
*Sent:* Wednesday, October 01, 2014 5:32 PM
*To:* Lance Parsons
*Cc:* galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] Jobs stuck in "new" state - Data Library
datasets to blame?
Are you attempting to upload datasets to a Data Library, and then
copy to a history and run jobs on them right away? I've run into
issues before where if I attempt to run a job on a dataset in a
library before it is finished being uploaded and processed, then the
job gets stuck in a queued state and never executes.
Aaron
On Wed, Oct 1, 2014 at 2:51 PM, Lance Parsons <lpars...@princeton.edu
<mailto:lpars...@princeton.edu>> wrote:
Recently, I updated our Galaxy instance to use two processes (one for
web, the other as a job handler). This has been working well, except
in a few cases. I've noticed that a number of jobs get stuck in the
"new" status.
In a number of cases, I've resolved the issue by downloading and
uploading one of the input files and rerunning the job using the
newly uploaded file. In at least one of these cases, the offending
input file was one that was copied from a Data Library.
Can anyone point me to something to look for in the database, etc.
that would cause a job to think a dataset was not ready for use as a
job input? I'd very much like to fix these datasets since having to
re-upload data libraries would be very tedious.
Thanks in advance.
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
___________________________________________________________
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/
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
___________________________________________________________
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/