Jason Stajich

Or you can concate them all into R1 and R2 files and give to `funannotate train` (which might be slow for a giant dataset)? But your approach should work too...

strange, not seeing this error but maybe we can test with the same data as the post.

Did you run setup to download and install the external database ?

But seems overall very few annotations - only 93 pfam hits ?

I just manually delete genes with these issues usually. did you work around?

can you provide more information on the operating system, version of python, version of funannotate you are testing. This tests and works on a variety of unix and osx machines

This seems outside the scope of funannotate. if you would like to build visualization tools with the output from annotation that is great but not the primary purpose of this...

it uses multi-threaded minimap2 - you can also try [AAFTF](https://github.com/stajichlab/AAFTF) which has a `AAFTF rmdup` step that Jon and I also wrote and ported from funannotate, it is nearly the...

please let us know whether you tried additional approaches but the clean step does a lot of comparisons if there are many individual contigs - it uses multiple threads I...

yeah metaeuk is not ideal - i would use augustus in BUSCO instead if you can. it can do further training on the prediction params. I am not convinced our...