Question: Information request about new storage system copy
gravatar for MR
24 months ago by
MR0 wrote:

Hello, I've been following the posts about the file copy... Five instances of the Tophat analysis which I have initiated have the same status: "This job is currently running" for 3 days. They were created within the last week.

My understanding is that they are in the queue and so I should not rerun. This is my first time using the Galaxy interface. In postings I have read that "When the banner is removed, all data will be available." Is there a relative timeline for this?

Also on the four instances of Tophat which have the green, finished status, the accepted_hits file gives this message: "An error occurred setting the metadata for this dataset. Set it manually or retry auto-detection"

Following directions from an earlier post I've initiated auto-detection but it seems to be without consequence. The status remains. Is this all due to the file copy to the new storage system? Should I simply wait for the banner to be removed? Thanks for any insight!

ADD COMMENTlink modified 24 months ago by Jennifer Hillman Jackson25k • written 24 months ago by MR0
gravatar for Jennifer Hillman Jackson
24 months ago by
United States
Jennifer Hillman Jackson25k wrote:


All datasets have been migrated to the new file system and the banner is removed. If errors result from non-upload related jobs, check the inputs. They may need to be reloaded.

For the longer queue time, jobs may be delayed for a day or so while everyone using gets their jobs going again. Other jobs will queue quickly - immediately or under 20 minutes.

Queue time also depends on the tool (and which cluster it is dispatched to) and how many jobs you have launched/queued in your account. Job launching is balanced across all accounts on this server. Other Galaxy servers may have different a configuration.

We advise to not stop/restart jobs since this moves them to the back of the queue (extending wait time). However, if upload jobs started when the banner was in place are still queued, those can be restarted. Upload jobs started after the banner was removed should be allowed to process as-is.

Please note that Tophat jobs were known to have unassigned metadata (output "Accepted hits", in particular). Use the link to auto-detect metadata for these jobs, and allow that to complete, before starting downstream jobs that use these data as an input. I am retesting this - and will update this post if that issue is now cleared after the recent changes.

Best, Jen, Galaxy team

ADD COMMENTlink modified 24 months ago • written 24 months ago by Jennifer Hillman Jackson25k

This is very helpful. Thank you Jen!

ADD REPLYlink written 24 months ago by misty.peterson0

Update: there are still issues you may run into. Follow for updates here:

ADD REPLYlink written 24 months ago by Jennifer Hillman Jackson25k
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