Phil Arevalo

Hi Matthias, Thanks for your comments! 1) I will look into this empty directory problem but I think @davevanins may have better insight into that. 2) I think right now...

I've added information on the parameters to the README which I've reproduced here. @davevanins might be able to provide more specific insights too! > ref_iso: identifier (filename without the extension)...

Hi Yun, I was unable to recreate this on my own system. I think one possibility might be that you may be running a newer version of `mmseqs2` than we...

Yes, I think this is an issue with the genome names being interpreted as integers and not strings. Do your genome filenames only have numbers (aside from the .fasta extension)?...

Hi Nick, Thanks for trying to incorporate it into Bioconda! I would like to resolve a couple of issues that have come up before making a release, but I hope...

@vinisalazar I've restructured the main module to work with snakemake and that has proven to be the most stable so far. The flexible genome module will need some work to...

Ah! Sorry about letting the other bug fall through the cracks. I will look into this.

Can you open a terminal and paste the output of `conda list -n PopCOGenT`? I just want to make sure that there's nothing odd in the installation.

Unfortunately, I've been unable to track this issue down. My best lead was that it had to do with the HPC having a competing environment which somehow takes precedence over...

At the time of publication, we had not tested this method with MAGs and did not have good intuition for how contamination might affect the results. Since MAG assembly methods...