Hi Evan,

If this is something that you rarely see and your filesystem is on a
network drive,
you could try setting `retry_job_output_collection` to 10 in the galaxy.ini
file.
This will let galaxy try to collection the output files 10 times,
which should help if there is some delay for the filesystem to be updated.

Best,
Marius

On 14 June 2017 at 22:02, evan clark <eclar...@fau.edu> wrote:

> Has anyone seen a similar error like this before. We are unsure if galaxy
> is causing the issue or it is being cuased by slurm as it seems galaxy is
> prematurely deleting a file.
>
> galaxy.jobs.runners DEBUG 2017-06-14 19:36:45,719 (3261/143577) Unable to
> cleanup /cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/
> 003/3261/galaxy_3261.ec: [Errno 2] No such file or directory:
> '/cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/003/3261/
> galaxy_3261.ec'
> galaxy.jobs.output_checker DEBUG 2017-06-14 19:36:45,725 Tool produced
> standard error failing job - [slurmstepd: get_exit_code task 0 died by
> signal
> ___________________________________________________________
> 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:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/
___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

Reply via email to