On Jan 5, 2012, at 1:10 PM, Ryan Golhar wrote:
>
>
> I discovered the problem. My pbs queue has a wall time restriction of 3600
> seconds.
>
> Is there a way to configure Galaxy to keep the job files for only failed
> jobs? I'd like to keep these two settings on, but find it unnecessary i
>
> In recent versions, the setting in the Galaxy config to keep job files is:
>
>cleanup_job = never
>
> I discovered the problem. My pbs queue has a wall time restriction of 3600
> seconds.
>
> Is there a way to configure Galaxy to keep the job files for only failed
> jobs? I'd like
>
>
>>
> I discovered the problem. My pbs queue has a wall time restriction of
> 3600 seconds.
>
> Is there a way to configure Galaxy to keep the job files for only failed
> jobs? I'd like to keep these two settings on, but find it unnecessary if
> jobs successfully complete.
>
The other option
>
> On Jan 5, 2012, at 11:46 AM, Ryan Golhar wrote:
>
> > I have three bam files that I'm trying to merge. The job runs for a bit
> then errors saying there is a problem. When I look at runner0.log I see:
> >
> > galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,193 (19) submitting
> file /home/g
On Jan 5, 2012, at 11:46 AM, Ryan Golhar wrote:
> I have three bam files that I'm trying to merge. The job runs for a bit then
> errors saying there is a problem. When I look at runner0.log I see:
>
> galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,193 (19) submitting file
> /home/galaxy/ga
...@gmail.com]
Sent: Thursday, January 05, 2012 10:46 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] PBS job failed: Unknown error: -10
I have three bam files that I'm trying to merge. The job runs for a bit then
errors saying there is a problem. When I look at runner0.log
I have three bam files that I'm trying to merge. The job runs for a bit
then errors saying there is a problem. When I look at runner0.log I see:
galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,193 (19) submitting file
/home/galaxy/galaxy-dist-9/database/pbs/19.sh
galaxy.jobs.runners.pbs DEBUG
