Non-deterministic clustering (possibly due to multi-threading) about ppanggolin HOT 4 CLOSED

Hi !
The fix has been included in PPanGGOLiN 2.1.1
Hope that will help you.

from ppanggolin.

Hi!

Thanks for pointing that out. I'm baffled about this because we added a check in the test dataset to make sure the number of clusters is as expected. I also remember a problem checking if gene families, representative genes, ... were in line with expectations. @Jmainguy will confirm, but the locally calculated cluster differed from the GitHub action.

I'm going to try what you suggest. If the problem persists, we could open an issue on the MMSeqs2 repository and work with them to solve it.

Thanks again

from ppanggolin.

Hi!

I found out that the clustering step was not the problem. The issue was in the writing step. When we write genes in the gene_families.tsv file, they are randomly ordered. I change the function to sort the gene families by size and gene by alphabetical order. This way, the clustering is the same between 2 runs.

You can check this PR #265

Also, I added a checksum to the GitHub action based on your suggestion.

Regards

from ppanggolin.

Thank you for troubleshooting! I will test out the new release.

from ppanggolin.