AlphaFold-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
2.0.0
Author / Distributor
Please see https://github.com/deepmind/alphafold
Description
From https://github.com/deepmind/alphafold: "This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. "
Running Program
Also refer to Running Jobs on Sapelo2
For more information on Environment Modules on Sapelo2 please see the Lmod page.
- Version 2.0.0, installed as a conda environment in /apps/gb/AlphaFold/2.0.0_conda/
To use this version of AlphaFold, please first load the module with
ml AlphaFold/2.0.0_conda
Once you loaded the module, an environmental variable called EBROOTALPHAFOLD is exported. It stores the AlphaFold installation path on the cluster, i.e., /apps/gb/AlphaFold/2.0.0_conda. The bash script run_alphafold.sh in installed in EBROOTALPHAFOLD/alphafold, and the 2.2TB of database files are in /db/AlphaFold (this is the directory that you need to use for the -d option of run_alphafold.sh).
Sample job submission script (sub.sh) to run run_alphafold.sh in a batch job (without GPU):
#!/bin/bash #SBATCH --job-name=alphafoldjobname #SBATCH --partition=batch #SBATCH --ntasks=1 #SBATCH --cpus-per-task=4 #SBATCH --mem=20gb #SBATCH --time=120:00:00 #SBATCH --output=%x.%j.out #SBATCH --error=%x.%j.err #SBATCH --mail-user=username@uga.edu #SBATCH --mail-type=ALL cd $SLURM_SUBMIT_DIR ml AlphaFold/2.0.0_conda bash $EBROOTALPHAFOLD/alphafold/run_alphafold.sh -d /db/AlphaFold [options]
An example of the required options to use are
bash $EBROOTALPHAFOLD/alphafold/run_alphafold.sh -d /db/AlphaFold -o ./test/ -m model_1 -f ./query.fasta -t 2020-05-14
Sample job submission script (sub.sh) to run run_alphafold.sh in a batch job (with GPU):
#!/bin/bash #SBATCH --job-name=alphafoldjobname #SBATCH --partition=gpu_p #SBATCH --ntasks=1 #SBATCH --cpus-per-task=4 #SBATCH --gres=gpu:1 #SBATCH --mem=40gb #SBATCH --time=120:00:00 #SBATCH --output=%x.%j.out #SBATCH --error=%x.%j.err #SBATCH --mail-user=username@uga.edu #SBATCH --mail-type=ALL cd $SLURM_SUBMIT_DIR ml AlphaFold/2.0.0_conda bash $EBROOTALPHAFOLD/alphafold/run_alphafold.sh -d /db/AlphaFold [options]
where $EBROOTALPHAFOLD is the environmental variable that stores the AlphaFold installation path on the cluster; [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.
Example of job submission
sbatch sub.sh
Documentation
Details are at https://github.com/kalininalab/alphafold_non_docker
ml AlphaFold/2.0.0_conda
bash $EBROOTALPHAFOLD/alphafold/run_alphafold.sh -h
Usage: /apps/gb/AlphaFold/2.0.0_conda/alphafold/run_alphafold.sh <OPTIONS>
Required Parameters:
-d <data_dir> Path to directory of supporting data
-o <output_dir> Path to a directory that will store the results.
-m <model_names> Names of models to use (a comma separated list)
-f <fasta_path> Path to a FASTA file containing one sequence
-t <max_template_date> Maximum template release date to consider (ISO-8601 format - i.e. YYYY-MM-DD). Important if folding historical test sets
Optional Parameters:
-b <benchmark> Run multiple JAX model evaluations to obtain a timing that excludes the compilation time, which should be more indicative of the time required for inferencing many
proteins (default: 'False')
-g <use_gpu> Enable NVIDIA runtime to run with GPUs (default: 'True')
-a <gpu_devices> Comma separated list of devices to pass to 'CUDA_VISIBLE_DEVICES' (default: 'all')
-p <preset> Choose preset model configuration - no ensembling (full_dbs) or 8 model ensemblings (casp14) (default: 'full_dbs')
Installation
Installed using a conda environment following the documentation at https://github.com/kalininalab/alphafold_non_docker
The database files are installed in /db/AlphaFold/
System
64-bit Linux