Hi Jennifer,
Things are going better in the main server of Galaxy since the beginning of this week: thanks for these last improvements !
However, I started worflows of NGS analysis last monday (30th of september) for two histories (I guess something similar to Zuzana's worflow). Since I started it, all the steps of the worflow are "waiting to run" ("grey status"). I tried many times to start them by clicking on "Resume paused jobs" (in the history wheel-tool menu), but nothing happened. As you said in your reply to Zuzana, NGS jobs are still in hold so far. Do you confirm me I ought to wait (and avoid cancelling the worflow to start a new one, as it would end up in more delay)?
At the same time, I am doing other NGS analysis with other histories (GATK Base Quality Recalibration and Unified Genotyper) and these jobs are working well. This time, I am doing all the steps sequentially, without worflows. Do individual NGS jobs run better than worflows or is it just variable from tool to tool ?
Thank you for reply and for all your constant efforts to maintain this very useful plateform in shape !
Fabrice
Le 03/10/2013 00:20, Jennifer Jackson a écrit :
Hi Zuzana,
Jobs queue individually. But different jobs may queue to different clusters, so if there are no dependencies, you may see jobs execute out of order. Workflows are still a benefit as this places jobs in the queue sooner than waiting for each job to finished (under normal circumstances
- not the extended queue times seen now during the server reconfiguration).
The banner on main provides updates about the status of Main, but right now NGS jobs are in hold. We expect these to start again tomorrow and then for the final stages of the upgrades to be complete within the next few weeks.
Apologies for the slow reply to your question,
Jen Galaxy team
On 7/24/13 2:33 PM, zuzmus wrote:
Dear Galaxy managers,
I would like to ask about the queuing rules for the workflows before processed on the server?
I use my customized Galaxy workflow which contains 22 following steps (basically, filtering, trimming and format change of NGS data). I guess the server is generally very busy during last weeks/months (?), so my job was waiting about 24 hours in a queue (which would not be a problem), and then the first step of the workflow was processed, but the following 21 is again/still waiting (already for another couple of hours...). It makes me wondering about the queuing rules because I expected that the whole workflow is queued as one job.. Then my question is if the whole workflow, once submitted, is listed in the queue, or does the following step queue only after the previous step is finished (which would mean to wait the whole queue for each step of the workflow...)?
I routinely used those wrokflows before (months ago) without any problems...
I tried to search similar question in the archive before I posted this one...
Thanks a lot for your answer,
My best
Zuzana Musilova
Zuzana Musilova, PhD. (zuzmus@gmail.com mailto:zuzmus@gmail.com)
Zoological Institute University of Basel Vesalgasse 1, CH-4051 Basel Switzerland - Europe
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