#!/bin/bash
#SBATCH --partition=nonpre        # Partition (job queue)
#SBATCH --requeue                 # Return job to the queue if preempted
#SBATCH --job-name=RAXML          # Assign a short name to your job
#SBATCH --nodes=1                 # Number of nodes you require
#SBATCH --ntasks=1                # Total # of tasks across all nodes
#SBATCH --cpus-per-task=25        # Cores per task (>1 if multithread tasks)
#SBATCH --mem=182000              # Real memory (RAM) required (MB)
#SBATCH --time=72:00:00           # Total run time limit (HH:MM:SS)
#SBATCH --output=slurm.%N.assembly.RAXML-NG-75-25.out  # STDOUT output file
#SBATCH --error=slurm.%N.assembly.RAXML-NG-75-25.err   # STDERR output file (optional)

#Sanity check
#raxml-ng --parse --msa mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.phylip --model GTR+G

#RAxML ML tree inference with 20 tree searches (25 random and 25 parsimony based starting trees)
raxml-ng --msa mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.phylip --model GTR+G --prefix T25 --threads 25 --seed 2 --tree pars{25},rand{25}