Trinotate error? See GTN Transcriptomics tutorials for alternatives!

usegalaxy.eu support
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1

GDay,

Trinotate jobs fail in Europe and Australia, with similar message:

.import Trinotate.TaxonomyIndex TaxonomyIndex" | sqlite3 Trinotate.sqlite
* Running CMD: wget "http://eggnogdb.embl.de/download/eggnog_4.5/data/NOG/NOG.annotations.tsv.gz"
--2025-10-03 04:22:07--  http://eggnogdb.embl.de/download/eggnog_4.5/data/NOG/NOG.annotations.tsv.gz
Resolving eggnogdb.embl.de... 194.94.44.170
Connecting to eggnogdb.embl.de|194.94.44.170|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2025-10-03 04:22:07 ERROR 404: Not Found.

History.

I see it for some time.

Thank you!

Igor

2

Hi @igor

I think this is expected. The source for the reference data is not available anymore due to the deprecated protocol. So, it ends up failing anywhere.

I last looked at this in July → Trinotate SQLite boilerplate unavailable on usegalaxy.eu?. For history, the tool sort of worked at EU/AU long ago but never at ORG (persistent SQLite issues). Now it won’t work anywhere due to the missing reference data (which would be 10+ years outdated by now even if located!).

We should probably get the tool tagged as deprecated on all the servers but there isn’t a good “meta” process for that (is a 1-off by admins, and can get stripped with the automatic tool updates). Maybe this will help to get it picked up → Meta Request: Tag Trinotate as a deprecated tool at all UseGalaxy servers · Issue #430 · galaxyproject/usegalaxy-playbook · GitHub.

3

Hi @jennaj

It must be a recent change: I see completed Trinotate jobs in September, this year. I mean Galaxy Australia.

Trinotate is used in a tutorial marked as Under development.

What alternative(s) to Trinotate do you recommend? InterProScan, eggNOG Mapper, FGENESH, something else?

Have a great day,

Igor

4

Oh! This is interesting. I wasn’t aware of the reference data being available, or with the current tool wrapper able to use it without running into that error. To solve this, I think asking the local administrators about how the configuration is different from the IUC wrapper/job container would be needed. This never worked at the ORG server, but the EU people might know more (I couldn’t get it to work there either, but maybe I tried it after the external tool was deprecated).

Then for

Those the ones I know about too.

The GTN also includes GOEnrichment and gProfiler GOSt in their examples – but these would work after the transcripts are mapped to knowns, similar to how annotateMyIDs works.

5

The tool has been deprecated by the authors and is no longer available! For ideas about alternatives, try Search results for 'trinotate' - Galaxy Community Help or see our Transcriptomics tutorials :graduation_cap: Transcriptomics / Tutorial List. For adventurous hosting on your own server, please see Trinotate SQLite boilerplate unavailable on usegalaxy.eu?.