Jason Stajich

We don't directly use this module (IO::Socket::SSL) so I am unclear where this would addressed. I think based on the inheritance this is probably best addressed in the module [Bio::DB::WebDBSeqI](https://github.com/bioperl/bioperl-live/blob/master/lib/Bio/DB/WebDBSeqI.pm)...

thanks for reporting a bug rather than just twitter rant! maybe others can look at this too @cjfields -- its been 15+ years with that code - I think this...

Chris Mungall wrote a gbk to gff script that used feature or name overlap to assign genes mRNA CDS to common parent group. It should be in scripts folder. I...

I haven't tested this yet myself but this seems like an appropriate update - is there a performance improvement or a particular bug this fixes?

FYI - success here with downgrade to 2.10 eg after building the env I forced the cutadapt version down to 2.x ``` conda install cutadapt=2.10 ```

Sounds like eggnog mapper isn’t installed in this image? Also genemark but that shouldn’t be fatal.

did you setup the channels in mamba or specify the channel on the cmdline? https://funannotate.readthedocs.io/en/latest/install.html#install ```mamba create -n funannotate -c bioconda -c conda-forge funannotate```

Its unclear if your system is killing the minimap run (due to resources?) is this running in a job manager HPC or on a laptop? This is inferred from the...

As far as I can tell this will work as expected - should we merge it @nextgenusfs or do we try for additional tests?

Two things. If you run pasa with MySQL server will vastly speedup pasa and update should restart at a checkpoint if you just resubmit the job. I assume you cannot...