nextgenusfs
funannotate remote does not recognise predict_results folder
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
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
The issue was with funannotate predict and biopython, it is discussed in more detail here: https://github.com/nextgenusfs/funannotate/issues/1000
having the same issue, have you found a solution yet? failing at iprscan and annotate.
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.
Also, make sure you install with conda as a whole new environment, my environment was created within another one, adding to the issue
what versions of anaconda, python,biopython, and funannotate are you using?
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