Alex Chklovski

Hi, there appears to be something wrong with your Diamond installation. Was your CheckM2 installation done through bioconda or manual installation? Can you install it into a fresh conda environment...

Hi, what's your diamond version? Can you create a conda/mamba environment manually using the CheckM2 .yaml file first, and verify DIAMOND works before installing CheckM2?

Hi, if you wish to download the database but not set it within CheckM2, would downloading it externally to the program and using it to set the CHECKM2DB variable be...

Next version will update to most recent DIAMOND release and reformat the database to work with that so that will hopefully fix some of these issues.

Hi, apologies for the late response. Does installing via conda/mamba fix this issue?

Please feel free to reopen if you have further information or error persists.

Thanks for catching this. Next version will have more thorough DIAMOND error handling.

Currently CheckM2 chunks both the diamond annotation (500 genomes per chunk) as well as feature vector generation & ML prediction (250 genomes per chunk) to avoid having a large memory...

Hi, Is the issue that you get different completeness/contamination values for the endosymbiont genomes in supplementary table 6? After testing checkm2 on these genomes, we subsequently added them to the...

Unfortunately the scikit-learn version is a hard requirement due to incompatible version-changes to pickled data scalers checkm2 loads. I am looking into getting rid of that, but for the moment...