running raxml-ng with 500 bootstraps

[Dowd Naik]

Hello,

Hope everyone is doing well this March. I am fairly new to working in the field of bioinformatics and creating phylogenetic trees. I was using Raxml only recently discovering the existence of raxml-ng. I need to create a phylogenetic tree with 500 bootstraps for an alignment of ~860 bacteria isolates. I am hoping that the raxml-ng will be able to help me with this. I just want to make sure I am running this correctly, I first ran

/network/rit/lab/andamlab/Dowd/raxml-ng --parse --msa core_alignement.phy --model GTR+G --prefix T2

which gave me * Estimated memory requirements                : 13794 MB

* Recommended number of threads / MPI processes: 16

SO I am running

#!/bin/bash

#SBATCH --job-name=raxml      # Job name
#SBATCH --ntasks=1                   # Run a single task
#SBATCH --mem=50gb                     # Job memory request
#SBATCH --cpus-per-task=8            # Number of CPU cores per task
#SBATCH --time=174:00:00              # Time limit hrs:min:sec
#SBATCH --output=raxml.log     # Standard output and error log

#source /network/rit/lab/andamlab/bin/miniconda3/etc/profile.d/conda.sh
#conda activate raxml
umask g+rwx
/network/rit/lab/andamlab/Dowd/raxml-ng --bootstrap --msa core_alignement.phy --model GTR+G --prefix T3 --threads 8 --seed 8 --bs-trees 500
exit 0

Is what I have done the correct way of running this? Any insight you have into this would be most appreciated. 

Have a good day,

Dowd Naik

[Alexey Kozlov]

Hi Dowd,

you can use more threads for this analysis with coarse-grained parallelization, please read:

https://github.com/amkozlov/raxml-ng/wiki/Parallelization

Best,
Alexey

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[Dowd Naik]

Hello Alexey,

Thank you for getting back to me, I will explore this option. Be safe and be well.

Sincerely,

Dowd