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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 <lparsons@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

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