Jobs running for unexpectedly long durations.

usegalaxy.eu support
1

Hello
I started a workflow on Jan 12 (7 days back). Some jobs worked while some are still in running. Small jobs like Krona plot is also running for 5+ days now.

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I attempted to run the Krona plot tool again on the Galaxy 13 file. It produced output within an hour.

Similarly my Flye assembly tool is also running for 5+days now. It would be very kind of you, if you can direct me to resolving this issue.

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Thank you
Shreyash

2

The above mentioned jobs are still running. The fly assembly as well as the Krona pie chart ploting tool are running now for 11 day. (The jobs are not queued, they are running for 11 days now). Starting a fresh run with Fly did not help either (It is running for last 5 days).
Similar case is observed in an older history, where the EggNOG mapper is now running for last 19 days. I request your kind advice on the subject.

Thank you!

Best regards
Shreyash

3

Hi @Shreyash_04

If your jobs are still running (executing), then you’ll need to let them finish or the job logs will be lost (in case of an error) along with the output (in case of success!).

The UseGalaxy.eu server will attempt to run even the largest of jobs, so you are working in the right place when using an assembler like Flye. And the server will try at least one rerun for failures, so this may be the automatic second run of those jobs if they failed the first time.

So … there isn’t much to do now except wait to see what happens. The public resources are seriously massive but not infinite, and some work will eventually be “too large” but you won’t know until these fully complete.

If you want to see what the server is processing, there is a graph linked from the homepage of the server. How to find it is in this screenshot – in short, go the homepage and scroll down a bit …

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4

Hi @jennaj

Thank you for your reply. I will wait for few more days. I have performed similar analysis with fly in past with similar data sets, it takes a maximum of a day to execute the job. I was concerned if it is something specific to my account. Specially as small jobs like the krona plot tool, which normally takes no longer than 30 mins is also running (Executing) for 13 days now.

Thank you again for your time. Will update here again in a week on the job status. At present they all are still running (executing).

Best regards
Shreyash

5

Hi @Shreyash_04

That sounds like a good plan.

If this continues, you could also ask the EU administrators directly to take a look at your jobs. The link to the Gitter chat is at the very bottom of the EU server homepage. They’ll let you know what info they need to find it.