Overview

RELION is an application for cryo-electron microscopy data analysis. It is used to reconstruct three-dimensional biomolecular structures through Bayesian-based image processing workflows.

This example demonstrates how to submit a RELION job in IEC and review the generated output files.

Procedure

Preparing Input Data

1. Go to EonKube > HPC > File Explorer.
2. Upload the required tutorial or project data into the user's home directory.
3. Extract the uploaded data if necessary.

   Example:

   wget ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion30_tutorial_data.tar
   tar -xf relion30_tutorial_data.tar
       

4. Create a result folder, such as gms_results, to store output logs.

Submitting the Job

1. Go to EonKube > Apps > Marketplace.
2. Open the RELION application page.
3. Click Submit.
4. Configure the required settings.
   • Basic Settings
     • Project: Select a Project from the drop-down menu.
     • Job Name: e.g., relion-job
     • App Version: GPU-4.0.1(MPI)
     • MPI: Enable if MPI execution is required
   • Resource Configuration:
     Configure control node and compute node resources according to workload requirements.
     Example configuration:
     
     • Control Node
       • CPU: 1 Core
       • Memory: 2 GiBs.
       • GPU: 1 GPU
     • Compute Node
       • CPU: 4 Core.
       • Memory: 4 GiBs.
       • GPU: 1 GPU
       • Node: 2 Nodes.
   • Command Settings: Enter the command to execute RELION. For example:
     • If you are using an administrator account, add the --allow-run-as-root flag if required by the runtime environment.

       mpirun --allow-run-as-root ... ...

     • Run a RELION import process within a Singularity container for processing electron microscopy movie files.

       singularity run --nv $APP_BINARY relion_import  --do_movies  --optics_group_name "opticsGroup1" --angpix 0.885 --kV 200 --Cs 1.4 --Q0 0.1 --beamtilt_x 0 --beamtilt_y 0 --i "relion30_tutorial/Movies/*.tiff" --odir relion_test_Import/ --ofile movies.star
       mkdir -p relion_test_MotionCorr
                   

     • Adjust $MPI_HOST and $NODE_NUM as needed for your environment.

       mpirun --host $MPI_HOST -np $NODE_NUM singularity run --nv $APP_BINARY relion_run_motioncorr --i relion_test_Import/movies.star --o relion_test_MotionCorr/ --first_frame_sum 1 --last_frame_sum -1 --use_own  --j 3 --bin_factor 1 --bfactor 150 --dose_per_frame 1.277 --preexposure 0 --patch_x 5 --patch_y 5 --eer_grouping 32 --gainref relion30_tutorial/Movies/gain.mrc --gain_rot 0 --gain_flip 0 --dose_weighting

5. Click on Create to submit the job.