Use checkm2 instead of checkm

[fplazaonate]

Hi,

First of all, thanks for developing ComeBin.
I was wondering if you had considered switching to checkm2 instead of checkm to determine the best settings for graph clustering?
Checkm2 is much faster than checkm (especially for low-completeness bins) and provide betters estimates.

Best,
Florian

[ziyewang]

Hi,

Thank you for your suggestion. I will test the effectiveness of CheckM2 before the next version update. For CheckM1, we used marker gene information and did not run evaluations for each result. But from what I understand about CheckM2, it might be necessary to run evaluations for each result.

Best,
Ziye

[RolandWirth]

Hi all,

The CheckM2 marker gene information may be useful for the newer Comebin version. However, integrating the CheckM2 program into the workflow may be problematic. The current version of CheckM2 will not run on some newer operating systems (conda version: 23.3.1; mamba version: 1.4.2; Python 3.8.19) due to a DIAMOND bug.
Here is the post about it: chklovski/CheckM2#100
It is advisable to wait for a newer version of CheckM2 if you plan to integrate it into Comebin.

Best,
Roland