AlphaFold

AlphaFold Overview

AlphaFold is a program to It is currently available as module on CURC Alpine. Please contact rc-help@colorado.edu if you would like to run AlphaFold on Blanca.

Running AlphaFold

Load the default AlphaFold module:

module load alphafold

View run options:

run_alphafold

AlphaFold Module

Loading the AlphaFold module does the following:

  • redirects temporary files from /tmp to /scratch/alpine/$USER

    • you can override this path by resetting TMPDIR after you load the module:

      module load alphafold
export TMPDIR=<path/of/your/choosing>

  • activates the AlphaFold conda environment

  • sets CURC_AF_DBS and CURC_AF_EXAMPLES environment variables (see ‘AlphaFold Databases’ and ‘AlphaFold Examples’ sections, below`)

  • creates a shortcut to the AlphaFold script so you can run the program with run_alphafold

AlphaFold Databases

The AlphaFold databases are located in /gpfs/alpine1/datasets/bioinformatics/alphafold. Note that this directory is not visible from a login node. Loading the AlphaFold module stores this path in CURC_AF_DBS.

AlphaFold Examples

Several example fasta files are located in /curc/sw/install/bio/alphafold/examples. Loading the AlphaFold module stores this path in CURC_AF_EXAMPLES:

ls $CURC_AF_EXAMPLES
dummy.fasta  multimer.fa  rcsb_pdb_7DDD.fasta  T1050.fasta

Example Job Script

This example job script below is saved in /curc/sw/install/bio/alphafold/2.3.1. You can copy it to any space you have write permissions and make the desired changes:

cd /projects/$USER
cp /curc/sw/install/bio/alphafold/2.3.1/alphafold_alpine.sh .

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --time=06:00:00
#SBATCH --partition=aa100
#SBATCH --qos=normal
#SBATCH --gres=gpu:1
#SBATCH --job-name=multimer_test
#SBATCH --output=multimer_test_%j.out
#SBATCH --ntasks=40
#SBATCH --mail-type=ALL
#SBATCH --mail-user=<your email address>

module purge
module load alphafold

#change directory
cd /projects/$USER

#run AlphaFold
run_alphafold -d $CURC_AF_DBS -o . -f $CURC_AF_EXAMPLES/dummy.fasta -t 2020-05-14 -m "monomer" -g true