Broccoli - infer with high precision orthologous groups and pairs of proteins using a mixed phylogeny-network approach

 1#!/bin/sh
 2#SBATCH -J broccoli
 3#SBATCH --partition 
 4#SBATCH --nodes=1
 5#SBATCH --ntasks-per-node=32
 6#SBATCH --time=120:00:00
 7#SBATCH --mem=480gb
 8#SBATCH --mail-type=BEGIN,END,FAIL
 9#SBATCH --output=.%j.out
10#SBATCH --error=.%j.err    
11
12
13module load FastTree/2.1.11-GCCcore-8.3.0
14
15ml Anaconda3
16
17ml DIAMOND
18conda init bash
19source ~/.bashrc
20conda activate binf
21
22cd $SLURM_SUBMIT_DIR
23
24python broccoli.py -dir /fastaFiles -threads 32 -ext '.fa' -path_fasttree /apps/eb/FastTree/2.1.11-GCCcore-8.3.0/bin/FastTree