Jason Stajich

have you run `bedtools intersect` on its own?

sure can - as long as they are closely related the RNA will align and it can generate genemodels, if the train step fails with these it is usually because...

Did you install gmap by conda. I don't even think it works as well as exonerate so we don't make it a default.

you are running the sqlite version to generate the db - might be that the path loaded is diff when you run interactively vs direct? might be good to test...

I think we can add something for it - I feel like we have to roll up our sleeves for some more comprehensive unit tests all around TBH... I'm happy...

can you check in what is in `annotate/predict_misc/ab_initio_parameters` something maybe did not download fully? can you just run `funannotate test -t predict` ? ``` for f in os.listdir(os.path.join(LOCALAUGUSTUS, 'species', aug_species)):...

I'm trying to see if I can get lighttpd installed on osx conda forge which is stopping me from testing on osx here.

@nextgenusfs have you been able to install things via conda okay on OSX?

yeah it won't for me right now - I think we could make an osx package for the tools which don't conflict and then provide instructions for pasa, augustus installs...

Can you check if there were any augustus predictions? It seems like there might be no high quality predictions? 50kb is also very large max intron size for fungi so...