Jon Palmer
Jon Palmer
I'm actively trying to fix another bug (that augustus compilation issue) on the latest docker image, it won't be stable for a little while, apologies.
do those have conda packages? those must be new dependencies I guess as I have others in here for GeneMark. I just haven't used it in a long time so...
Is this MCE::Mutex? https://anaconda.org/bioconda/perl-mce
Okay, well I just pushed those two perl modules in last commit, the docker image should have them when it finishes building in ~1 hour or so.
Thanks, yes I know about that. That script is very very old and I should probably label it "unsupported", it needs a complete rewrite which I don't have time to...
Seems like it failed extracting gene models from the GFF file you passed as PASA results. Was that PASA/transdecoder GFF3 file directly or something else?
You can pass external gene predictions to --other_gff, but they need to be proper gene predictions on your actual genome assembly.
Thanks, I'm not sure exactly why this would happen, but perhaps related to setting the 0 weights: `--weights augustus:2 pasa:10 snap:0 genemark:1 glimmerhmm:0`. If you run the test data and...
Currently only standard genetic code is supported. It might be possible to add at some point, but it is more of an issue with the de novo gene prediction algorithms...
It's not a simple fix in the sense that I think only Augustus can use alternative translation tables, thus you'd lose the benefit of running multiple de novo predictors and...