Hi all, since yesterday I have a problem with running “Flye” genome assembler on https://nanopore.usegalaxy.eu. It remains in the “This job is waiting to run” status for hours, while other tools start running without any problem, but only if I delete the blocked Flye job first. I would be grateful for any help. Thank you !
Like most assembly tools, the Flye tool is computationally expensive. That means the job requires more resources, and will tend to run longer than other tools.
When working at a public server, your own Flye jobs are running on shared resources also used by others to run these larger and longer running jobs. So, some patience is needed.
Practically, this means leaving the jobs “queued” and allowing them to run to completion.
Each tool has different processing requirements … and that can include “upstream” jobs. There is a limit on how many concurrent jobs each person can run. Getting jobs into the queue, then allowing them to complete, is the fastest way to process work for anyone. That is what a workflow will do for you. A workflow queues everything at once – then processes those jobs in a stream while you are away.
If you are still in a pre-workflow stage, then the best advice is to queue up as much as you can, set a notification, then come back later. Deleting and rerunning jobs puts all new jobs at the very back of the queue, each time, and if done quickly enough no jobs may ever have a chance of processing!
I’m adding some tags to your post that link to other similar Q&A.
Thank you very much for your reply. I understand better now. It’s just that I hadn’t had this problem before when I was launching Flye.