When attempting to run AlphaFold on the HPC, you might be confronted with a variety of errors, originating from several sources. Most commonly, they will be a result of a wrong configuration or resource exhaustion (e.g., when running large proteins or proteins with too large MSAs). The most common errors are enlisted below, along with possible workarounds to solve them.
You will find the errors that are described in two possible locations:
At submission time (qsub), the command line will reply with an error specification
In the error file that is generated for each job running on the HPC. This file can be found in your $VSC_DATA/alphafold directory, and will be named <job_name>.e<job_id> (for instance: example_run.e1502930). Display its contents with less or cat. The actual error message is most often found at the bottom of the file.