Jason Stajich

> I have the same problem the prediction folder failing? -what folders are created in the directory? Does predict_misc get created. @Midreancgle the spaces in your quoted errors are hard...

Troubleshoot by doing this outside funannotate this is external dependency so you can work on this outside the prog. which augustus It doesn’t look like you compiled a working augustus...

1. Stranded would depend on whether it was a strand-specific library prep or not. You [can guess](https://www.biostars.org/p/98756/) whether it was strand-specific with some analyses like [rseqc](http://rseqc.sourceforge.net/) - see [infer_experiment.py](http://rseqc.sourceforge.net/#infer-experiment-py) *...

this seems like it could be transient filespace usage or the files are cleaned up after funannotate aborts. I'd check the input folder size and/or monitor as you run funannotate...

its hard to debug it specifically unless CQ gives you more details - I assume if you run CQ outside of funannotate you still see the error message. your genome...

yes exactly - we use a system installed one not bioconda one.

Usually if you add conda-forge channel when installing Augustus in first place it gets it added?

Would be good to add this issue as an alert to @bioconda recipe for augustus too?

agree I get these errors too - I think we need to not trust eggnog as much perhaps. Wondering if IPR are more often consistent - so I'll be curious...

There is a way to do exonerate in server mode this might help. https://www.animalgenome.org/bioinfo/resources/manuals/exonerate/server.html