Predicting a single protein structure using Alphafold on Notos
Setup
- Copy the alphafold folder from /mnt/beegfs/alphafold/alphafold to your home directory
- When you log in to notos you are automatically in your home directory
- Run the command below to copy the folder into your home directory
cp -r /mnt/beegfs/alphafold/alphafold/ .
- This folder has all the required updates to run alphafold successfully
- Locate the folder named docker by running the command
cd alphafold/docker
- Open run_docker.py by running the command
vi run_docker.py
- Press i to insert and make edits to the file
- Change the destination folder output_dir on line 49 to a folder you wish the results are saved into
- Make sure you have sufficient read and write permissions for the output_dir folder
Running Alphafold
- To run alphafold, go back to the home directory by running the command
cd
- Type the command
python3 ~/alphafold/docker/run_docker.py --fasta_paths=path_to_sequence --max_template_date=YYYY-MM-DD --data_dir=/mnt/beegfs/alphafold/databases
- For example:
python3 ~/alphafold/docker/run_docker.py --fasta_paths=T1050.fasta --max_template_date=2020-05-14 --data_dir=/mnt/beegfs/alphafold/databases
- For optimized performance use the preset reduced_dbs. For example:
python3 ~/alphafold/docker/run_docker.py --fasta_paths=T1050.fasta --max_template_date=2020-05-14 --model_preset=monomer --db_preset=reduced_dbs --data_dir=data_dir=/mnt/beegfs/alphafold/databases
- You can use the date variable for the max_template_date by running the command
today = `date +%Y-%m-%d`
and setting max_template_date tomax_template_date = $today
- For example:
- Other presets and options can be found here
Using a GNU screen
To be able to detach and disconnect from a process without interrupting the procedure use GNU screen sessions:
- Follow the setup process above
- To start a named screen session, type the following in your console
screen -S session_name
- Run the required alphafold commands
- To detach from a linux screen session, press
Ctrl+a d
- To get the list of current running sessions, type the following
screen -ls
- To reattach to a linux screen, type the following
screen -r session_name
- More on GNU screen sessions can be found here.