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:*[email protected]
[mailto:[email protected]] *On Behalf Of *Aaron Petkau
*Sent:* Wednesday, October 01, 2014 5:32 PM
*To:* Lance Parsons
*Cc:* [email protected]
*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 <[email protected]
<mailto:[email protected]>> 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
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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
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