Shing Hei Zhan

Thanks, @EnzoAndree . It is strange, because how far I get in terms of downloading 153 schemes varies from run to run. Once I got as far as 30%, and...

Is this task supposed to consume a lot of memory? If so, it would be nice to mention in the README.

Thanks. I created a fresh environment with Python 3.12 and reinstalled fastmlst, but I am still encountering this problem. I'll create an issue once i get a better handle on...

I have managed to download all the schemes when running fastmlst on an older MacBook Pro, which doesn't use Apple Silicon. It seems it may have to do with the...

It turns out that some setup is incorrect with my laptop, and has nothing to do with fastmlst. Thanks for your help @EnzoAndree.

Thanks, Adelme. A related matter. I noticed that the parameter description for `dup_margin`[here](https://github.com/labgem/PPanGGOLiN/blob/f3ba6a1f33256f19175b570c4b711bb8970d0365/ppanggolin/formats/writeMSA.py#L25) doesn't seem quite right. I think that it should be the same as the parameter description [here](https://github.com/labgem/PPanGGOLiN/blob/f3ba6a1f33256f19175b570c4b711bb8970d0365/ppanggolin/geneFamily.py#L427)....

Thank you for the explanation. I checked whether "The file is likely equal between the different "input genome" output directories" for a few input genomes. But it didn't seem to...

Also, I was referring to https://github.com/labgem/PPanGGOLiN/blob/f3ba6a1f33256f19175b570c4b711bb8970d0365/docs/user/Outputs.md#gene-families-and-genes, which doesn't seem to exist anymore, in https://github.com/labgem/PPanGGOLiN/blob/f3ba6a1f33256f19175b570c4b711bb8970d0365/docs/user/projection.md

I have the following code produces a toy ts with 101 individuals, which were then split into a ref. panel of 100 individuals and a query set of one individual,...

Should we put those files in a new directory named, say, `python/tests/data/beagle/`?