AlphaFold on Jetstream2

This repository contains scripts and instructions for running AlphaFold on Jetstream2 at Indiana University.

Directory Structure

• FASTA_Temp/: Place your input FASTA files in this directory. The script will process all .fa files in this directory.
• OUTPUT/: The results of AlphaFold runs will be stored here.
• run_alphafold.sh: The automation script that runs the MSA and strcuture prediction.
• design_tools/: Contains the GPU and MSA scripts that are used by the run_alphafold.sh script.
• singularity.d/: Contains the runscripts and configuration files for the Singularity container. Users should verify the contents of this directory under ".singularity.d" in their built container, especially the runscript file, to ensure the correct entry point for AlphaFold is defined. (Ensure (.) dot files are visible.) If missing or incorrect, users may need to manually add or modify these files.

Main Script: run_alphafold.sh

This script automates the process of running AlphaFold for multiple input sequences. Here's what it does:

1. Sets up necessary directories and log files.
2. Iterates through all .fa files in the FASTA_Temp/ directory.
3. For each file:
   • Checks if MSA has already been generated (looks for features.pkl).
   • If not, runs the MSA generation script (run_alphafold-msa_2.3.1.py).
   • Runs the GPU prediction script (run_alphafold-gpu_2.3.2.py).
   • Logs CPU and GPU usage during the run.
   • Records execution times for both MSA generation and GPU prediction.

Setup Instructions

1. Install Apptainer (formerly Singularity):

   • For Ubuntu/Debian:

     sudo apt update
     sudo apt install -y software-properties-common
     sudo add-apt-repository -y ppa:apptainer/ppa
     sudo apt update
     sudo apt install -y apptainer

   • For CentOS/RHEL:

     sudo yum install -y epel-release
     sudo yum install -y apptainer

   • For macOS (using Homebrew):

     brew install --cask singularity

   • For other operating systems or detailed instructions, visit the official Apptainer documentation.

2. Verify the installation:

   apptainer --version

3. Download the Singularity image:

   • Option 1: Download from Sylabs (https://cloud.sylabs.io/library/prehensilecode/alphafold_singularity/alphafold)
   • Option 2: Download from the AlphaFold website

4. Build the Singularity container in your repository.

5. Verify the contents of the .singularity.d directory, especially:

   • runscript
   • Singularity
   • startscript
   • Other relevant files

6. Check your version of hhblits:

   hhblits --version
   

   If you get an "illegal command" error, you need to update hhblits. You can get it from: https://github.com/soedinglab/hh-suite.git

7. Installing hhblits:

   a. Clone the repository:

   git clone https://github.com/soedinglab/hh-suite.git

   b. Create and navigate to the build directory:

   mkdir -p hh-suite/build && cd hh-suite/build

   c. Configure the build:

   cmake -DCMAKE_INSTALL_PREFIX=~/hh-suite ..

   d. Compile and install:

   make -j 4 && make install

   e. Use the path as hh-suite/bin/hhblits and pass through --hhblits_binary_path into the gpu and msa scripts.

8. Update hhblits paths in the following files:

   • /home/vmathew/Desktop/gitrepo/JetstreamAF/design_tools/run_alphafold-gpu_2.3.2.py
   • /home/vmathew/Desktop/gitrepo/JetstreamAF/design_tools/run_alphafold-msa_2.3.1.py

   Update the following line in both files. If you're not updating hhblits, remove the following lines from both files:

   hhblits_binary = os.path.expanduser('~/hh-suite/bin/hhblits')

   f'--hhblits_binary_path={hhblits_binary}',

Running AlphaFold

1. Ensure all databases and dependencies are correctly set up.

2. Ensure the following python scripts under design_tools:

   • For GPU version: run_alphafold-gpu_2.3.2.py
   • For MSA version: run_alphafold-msa_2.3.1.py

3. Modify the scripts as needed to match your specific Jetstream environment and paths.

Important Notes

• Make sure you have the necessary permissions to run Singularity containers on Jetstream.
• Adjust paths in the scripts to match your Jetstream directory structure.
• Ensure you have sufficient storage and computational resources allocated for running AlphaFold.

Troubleshooting

If you encounter any issues:

1. Check the Singularity container's log files.
2. Verify all paths and environment variables are correctly set.
3. Ensure all required databases are accessible and up-to-date.