Jason Stajich

Hi 0- this would really be an antismash question, this tool is just parsing the results. I would encourage you to look at the html report that is in the...

if you want to upload those GBK files as an attachment we can test it locally - it sounds like a python/GO error in a dependency? BTW @nextgenusfs - I...

I made a test fix on a branch as [bfcecf3](https://github.com/nextgenusfs/funannotate/commit/bfcecf3f004e47ad04893e0843602fe161c1195c) I think this might be able to solve that - I still need to test same code as @SolayMane can...

@SolayMane you can try again with `python -m pip install git+https://github.com/nextgenusfs/funannotate.git` to get latest version from master branch - should be 1.8.16

You could just run repeatmasker outside of funannotate and give the masked file to predict and compare. I generally have stopped running masking within funannotate as I end up combining...

you can check what the `#!/usr/bin/perl` or `#!/usr/bin/env perl` in the `/mydir/software/gmes_linux_64_4/gmes_petap.pl` file - depending on if you have a conda env for your perl with the modules installed you...

generally we build a conda env for installation and then all the dependencies are part of that environment but if you are using external tool like genemark it will cause...

not sure what `**I had to go with the default species because I kept getting errors when I would change it.` - can you clarify where you had trouble with...

Can you restate your problem. I don’t understand what you are stuck on now. The long run time is not unexpected for a db or 35M protein alignments to sort...

this indicates where the training set for training the gene predictor(s) comes from. This would be set to pasa because you had done a `train` step before running predict: based...