RAxML Example

About

For information on RAxML, see the RAxML documentation

Example

#!/bin/bash
#SBATCH --job-name=RAxML-Example
#SBATCH --ntasks=8
#SBATCH --nodes=1             
#SBATCH --time=00:01:00   
#SBATCH --partition=standard
#SBATCH --account=YOUR_GROUP

module load raxml gnu8 openmpi3
date
mpirun -np $SLURM_NTASKS raxmlHPC-MPI-AVX2 -s phylip_sample.phy -n output_tree.tre -f a -m PROTCATBLOSUM62 -x 12345 -p 12345 -N 1000
date

Script Information

This RAxML script uses 8 CPUs and sets the following parameters:

Command	Description
-s phylip_sample.phy	Input file
-n output_tree.tre	Output file
-f a	Select algorithm. In this case, rapid boostrap analyses and search for best-scoring ML tree in one program run
-m PROTCATBLOSUM62	Model of substitution
-x 12345	Specify an integer number (random seed) and turn on rapid bootstrapping
-N 1000	Specify the number of alternative runs on distinct starting trees

Script Submission

(puma) [netid@junonia ~]$ sbatch raxml_example.slurm 
Submitted batch job 1694264

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