Dear all,
I tried to run a GO Enrichment analysis with the datasets provided in the tutorial (https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/goenrichment/tutorial.html). Nevertheless, I get back an error message in the initial graph and result files indicating: tool error; an error occured with the dataset; Failed to find or download one or more job outputs from remote server.
Does anybody have a solution for this issue?
Thanks a lot and best regards
Max
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Unfortunately I don’t have a solution, but I had the same problems with my own data. I got either the same error as Max described or that there was a mistake in one line of the obo file. I tried to reanalyze a datasets which I had successfully analyzed before (same tool, a few month ago) once more- same problem. Therefor I downloaded the trainings-datasets from the tutorial and got the following error: org.obolibrary.oboformat.parser.OBOFormatParser warn
WARNING: LINE: 475828 accepting bad xref with spaces:<MetaCyc: RXN-15910> LINE:
xref: MetaCyc: RXN-15910. Could there be something with the GO Enrichment tool?
Christiane
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Hi @Max @Christiane
Thanks for reporting the error and for all the tests. This does sound like either 1) a problem with the tool itself or possibly 2) a problem with server/cluster/resources running that tool.
For any urgent work, you could try running the tool at a different public Galaxy server to see if that resolves the error.
I’ll also be giving this a test and replying with updated info.
Ping to one of usegalaxy.eu admins in case there is a known issue I missed: @wm75. They may ask for a bug report.
Thanks!
Update Jan 25, 2021
The tool is working correctly at usegalaxy.eu again. Try a rerun for any jobs that failed (any error) or that have been queued for longer than a few days (the latter will likely never run).
For reference, the example history with the first few steps of the tutorial completed now includes a successful GOEnrichment run from today (Jan 25), and the two prior runs of that tool still in a queued state that will likely never resolve/execute (Jan 15 + Jan 18 tests): Galaxy | Europe | Accessible History | test GOEnrichment
Thanks @Christiane for reporting the problem!!
Update Jan 19, 2021
This tool is running slowly at UseGalaxy.eu right now – so no results there yet. That admin team is looking into it. The server may just be busy.
The immediate workaround is to run the tool/tutorial at UseGalaxy.org instead for now. Test history with the first few steps of the tutorial completed: Galaxy | Accessible History | imported from archive: test GOEnrichment
Update:
Apologies for the delay.
We are re-testing the tool and tutorial after a few recent updates (both the tool, and Galaxy itself).
A test history with the tutorial data and the first few steps (including GOEnrichment) are currently running. https://usegalaxy.eu/u/jenj/h/test-goenrichment
Let’s see how that test works out and follow up from there.