Phylophlan is running too slow when mapping DNA


I am interested in using phylophlan to construct a phylogeny of several genomes that belong to one genus (using all isolated genomes, MAGs and some reference genomes).

Phylophlan runs correctly using config from tutorial 05 (it gives bkp files), but the DNA mapping step is particularly slow. I am providing around 100 genomes, and using diversity medium, --fast flags and 24 cores on a modern AMD Threadripper workstation. So far, it only mapped ca. 15 genomes in 3.5 days. I was not expecting it to be that slow according to the documentation.

Do you think something could be wrong or something can be modified?

Thanks a lot

Hey, @eperezv I am facing the same issue. I have more than 2000 MAGs but it is taking a very long time in mapping the DNA.

Please do post if you modify something and it works out!


Hello. Yes, I will post if I find some workaround.

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Dear all, thank you for using PhyloPhlAn and reporting this.

I’m afraid I’m experiencing the same issue but this is a bit independent from PhyloPhlAn. In particular if the mapping step is carried out by diamond. It is very likely you have installed diamond version >=2 and in comparison to the first version, it is much slower. However, this is likely due also to a bug present in the first version that was recently discovered, you can read more about this here: Announcing HUMAnN 3.6 (Critical Update).

Apologies for not being more helpful in this case.

Many thanks,

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