raxml_G1_species_tree_9_taxa.srun

#!/bin/bash
#SBATCH --partition=longfat        ### Partition (like a queue in PBS)
#SBATCH --job-name=WG_tree_G1_9_taxa      ### Job Name
#SBATCH --output=WG_tree_G1_9_taxa.out         ### File in which to store job output
#SBATCH --error=WG_tree_G1_9_taxa.err          ### File in which to store job error messages
#SBATCH --time=4-00:00:00       ### Wall clock time limit in Days-HH:MM:SS
#SBATCH --nodes=1               ### Node count required for the job
#SBATCH -n10     ### Number of tasks to be launched per Node

# This command was used to run raxml and obtain the whole genome phylogeny

cd /projects/streisfeld/mchase2/standard-RAxML-master/

./raxmlHPC-PTHREADS-SSE3 -T 10 -m GTRGAMMA -p 1689131 -s /projects/streisfeld/mchase2/genome_reseq/genomeV1/var_calls/genome_V1/pairwise_comps/all_9_taxa_G1_vars.phylip.phy -w /projects/streisfeld/mchase2/genome_reseq/genomeV1/corr_landscape/trees/ -n WG_tree_G1_9_taxa