GTDB Forum

Performance of FastANI step

[2020-10-23 12:46:52] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
[2020-10-23 12:46:54] INFO: Calculating RED values based on reference tree.
[2020-10-23 12:47:11] INFO: Calculating average nucleotide identity using FastANI.

Firstly thanks for such a wonderful tool.
I’ve got over 100000 genome waiting for classification and I noticed that the FastANI step did NOT use as many cores/threads as I set in the command (–cpus 34), which made the process extremely slow. I use FastANI alone as well and am sure it supports multi-threading, so I’m wondering if I miss something here that this step was only processed by 1 thread.
Many thanks.

Hello, this will be resolved in the next release (1.4.0). For more information please see here.