Extremely long runtime due to OrthoMCL

[ghost]

I am running companion locally on a distributed cluster environment. While most steps can be easily parallelized and are completed within a few hours, the step nf-run_orthomcl runs for about 3 days on rather small (30MB) genome. Is this run time expected? I have been looking through the code, but it seems the tool is inherently unable to even use multiple cores.

Running companion through the web interface however does not nearly take as long, so I am wondering whether it can be optimized after all. I am using a custom genome locally, which is not available on the web version.

Thanks for your contribution to the field!