Long run time for phyml script - phybreak3.MSAsubset_runPhyML.py

[npbhavya]

Hi,

We are currently running the core_gene_sweep module, and stuck at third step which is running phyml. Do you have any suggestions on how to make this step run quicker, maybe increasing the number of threads or run them in parallel.

Our dataset includes 53 genomes, and according to phyml stats file, the number of datasets to run through is 108,133. So at the current pace, the script would take more than 20 days to complete running. Below is the command being run,

~/.local/bin/phyml -i PopCOGenT/src/core_gene_sweeps/output2align/phy_split/bovienii_core_genes.phy -n 108133 -q -m JC69 -f e -c 2 -a 0.022

Thank you, Bhavya