Jon Palmer

For degenerate nucleotide alignment, I'm doing the following in python which seems to work. Thanks for implementing the feature. I posted this in case it helps you with any tests,...

Fantastic thanks -- I'll give it a try and see if I find an improvement.

Brilliant -- I just needed to also edit at the qualcomp lines below -- ie the hp_compressed error rate function. Hopefully that looks correct to you? https://github.com/nextgenusfs/isONclust/blob/master/modules/cluster.py#L291-L314

It appears to say that `tbl2asn` failed in generating the genbank file. Do you have the log files for this run by chance? There is usually more information in the...

This is a compilation issue with Augustus with your system. This method is required for BUSCO to work. What OS are you on? Probably need to try a different conda...

In the docker image I can't reproduce (my dev machine is Mac so only linux test I have is docker), it installed this version of augustus (so same as yours...

Okay, so something must have changed in last build after I pushed commits yesterday, I can finally reproduce. Not sure what the problem is yet, will update here when its...

Okay, the docker image is finally working again. The workaround was to use Debian apt-get to install augustus (be sure to change/update the AUGUSTUS_CONFIG_PATH from the conda version if you...

@Midreancgle what is the output of `funannotate species`, also `augustus --species=help`. and `ls $AUGUSTUS_CONFIG_PATH`. I think you might just need to re-run `funannotate setup` if the version of augustus changes...

Those instructions were specific for macOS. Im not sure if the Augustus executable is static so compiling on one machine to run on another might not work. Generally this is...