Jon Palmer

Apologies. Conda/mamba is quirky. And the dependencies for funannotate are difficult. When I can't solve its usually because the base environment has packages installed in it which messes up the...

Apologies I've not had a chance yet to dig in. But on the surface it looks like BUSCO perhaps failed. Can someone share a genome and the corresponding `out/predict_misc/busco.final.gff3` --...

Thanks @jpaulsen0623, doesn't appear to be anything obviously wrong with this file. From this error report seems like error is emanating from Augustus.. https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?t=33 Is Augustus installed from conda? Anyway...

Yeah, that build seems to be the problem. Need to install a different build or install Augustus a different way. Funannotate only cares that it's in the PATH, it doesn't...

Was originally written for EVM v1.1 -- EVMv2 re-organized the code -- I thought I had it working but maybe not. I don't have the time/bandwidth to keep up with...

Download urls are here: https://github.com/nextgenusfs/funannotate/blob/master/funannotate/downloads.json See if you are able to manually download one or a few with `wget`

The max intron length should be set to 3 kb. Depends on how you ran it of course.....

Unlikely thru conda as too many dependencies. Funannotate2 will probably be possible, just haven't had the time to actual finish it.

What was the source of the input GFF?, it is likely a formatting issue. You can try to clean it up with GFFtk sanitize.

Are these two separate `augustus` installs? Can you look at the specific build numbers from conda? I'm guess there is an issue with the build version in 1.8.17 install. If...