iPHoP job running for 6+ days on Galaxy Europe (880 genomes)

[jennaj]

Welcome @afiaanjum_7

It sounds like your job is in the execution phase (yellow dataset) which is great! That means it has passed through queueing (gray dataset) and has been dispatched to the clusters.

@jennaj

When working at UseGalaxy.org, UseGalaxy.eu, or UseGalaxy.org.au, your analysis jobs execute at large scale academic clusters. Hundreds of thousands of jobs process each month!

• Use a Workflow for batch work.
• Allow queued (grey color) and executing (yellow-orange) datasets to finish processing.
• Deleting and rerunning puts your job back at the end of the queue again!
• Job priority is the exactly the same for everyone.
• Be patient. Galaxy is a free service, when a lot of people are using it, you may have to wait longer than usual (especially for ‘big’ jobs, e.g. alignments).

While a job is running, there won’t be any output to report back to the Galaxy application except for some timestamps on the job details view. This is a bit different from running a tool on your own computer where there might be standard error logs reporting progression through the algorithm. Once your job completes, you’ll get back those logs, and the standard outputs, plus the output datasets.

Then for this part, you are correct!

@afiaanjum_7

Since the dataset is quite large, I expected it to take some time

The job runtime of 6 days for ~880 viruses with this tool doesn’t seem unusual when working at the public clusters. The EU team didn’t reply yet, probably because this doesn’t seem odd so far. There isn’t an easy way to check the scientific progress of a running job and if there was a technical problem, it would fail and report that back. So, the best advice is to let this run to completion! Even if it eventually fails, that is how to get the logs.

And, the server itself seems to be processing lots of work! → How to see the UseGalaxy.eu job queue statistics

I see a job running with your target tool_id. This is probably yours!

I know this isn’t super satisfying but it is best I can provide unless the EU team jumps in with more advice. The EU server is a bit special in that jobs can run for an indefinite amount of time. I would let this keep running since stopping and restarting will lose the progress and the logs.

Hope this helps! And we can follow up more if this runs for too much longer, ok? The first few days were likely queuing time, so this might have only been “executing” for a day or two so far.