Jackson M. Tsuji

@SilasK @omrctnr I'm not sure if this helps, but a while ago (e.g., using ATLAS 2.8.2), I also noticed non-optimal behaviour of some rules in the QC module. Unfortunately, I...

@SilasK I've done a little work on optimizing the min mapping ID threshold, but nothing particularly comprehensive. I found that 0.76 can cause cross-over read mapping between related bins, especially...

@SilasK Thanks! I haven't tried using the 'best' mode but think it would be good to explore as the default setting for ATLAS. Using the 'best' mode could reduce noise...

@SilasK Interesting -- I've never run into that cyclic dependency error before. (Also, I regularly look through the BAM files output by ATLAS to link unassembled read analyses I do...

@SilasK My primary reason for using `source: genomes` is that it is very easy to relate the annotation data to the MAG data. You can easily relate the gene cluster...

@SilasK Thanks for the advice to look for `genomes/annotations/gene2genome.tsv.gz`! I'll take a look for it when my ATLAS run finishes. It should be okay to remove the `source: genomes` option...

@SilasK I took a look at `genomes/annotations/gene2genome.tsv.gz`. Unfortunately, like you mentioned, this file does not relate the exact Gene ID (from the Genecatalog) to the ORF ID in the MAG....

@SilasK Thanks for the helpful information! That is good to know that you are hoping to make the Genecatalog more independent of the genomes workflow long-term. (Trying out PLASS would...

I encountered the same issue while working with mmseqs version [14-7e284](https://github.com/soedinglab/MMseqs2/tree/14-7e284) and GTDB r214, using a Linux server (Ubuntu 22.04 LTS; CPU with SSE/AVX2 support and 512 GB RAM). Although...

@milot-mirdita Thanks for the quick response and for the data type fix! I tested the latest master branch, and the `gtdb.lookup` file seems to be correct now after running `mmseqs...