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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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funannotate remote does not recognise predict_results folder #1043

Open ydanylko opened 1 month ago

ydanylko commented 1 month ago

Are you using the latest release? Funannotate 1.8.15 with all dependencies installed properly (except optional genemark), as is stated in the tutorials and documentation

Describe the bug When running funannotate iprscan the predict_results folder works fine as the "funannotate folder" named in the documentation, however, when trying the same with funannotate remote -m antismash, it gives the following error:

Properly formatted 'funannotate predict' files do no exist in this directory

What command did you issue? /mnt/studentfiles/2024/2024MBI02/mambaforge/envs/funannotate/bin/funannotate remote -m antismash -e (removed my email for privacy reasons) -i /mnt/studentfiles/2024/2024MBI02/project/funannotate/spp1/predicted/predict_results/ -o /mnt/studentfiles/2024/2024MBI02/project/funannotate/spp1/antismash/

Logfiles The log file is attached

OS/Install Information I can provide this later, but rest assured all is properly installed and working except funannotate remote funannotate-remote.log

ydanylko commented 1 month ago

I decided to move on to funannotate annotate but this resulted in the same issue. I have uploaded the contents of my predict_results folder at the link below (compressed folder too big to upload here): https://we.tl/t-rm9rEo50QD

ydanylko commented 1 month ago

The issue was with funannotate predict and biopython, it is discussed in more detail here: https://github.com/nextgenusfs/funannotate/issues/1000

Okompath commented 2 weeks ago

having the same issue, have you found a solution yet? failing at iprscan and annotate.

ydanylko commented 2 weeks ago

I reinstalled completely, downgraded biopython as is posted there and indeed some aspects of funannotate like eggnog still fail. I would run eggnog and interproscan on the web (galaxy and eggnog website). If you reinstall at least annotate might work. But honestly, compared to NCBI quality my outputs were incredibly low quality. I would advise using a different program entirely honestly.

ydanylko commented 2 weeks ago

Also, make sure you install with conda as a whole new environment, my environment was created within another one, adding to the issue

Okompath commented 2 weeks ago

what versions of anaconda, python,biopython, and funannotate are you using?

ydanylko commented 2 weeks ago

I can't give a full list right now, but I was using biopython 1.79, it would not work otherwise. Do not attempt to install eggnog as it will downgrade to biopython 1.76, just use the webserver