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Here are the instructions to run AlphaFold in an interactive session. Since AlphaFold takes hours to run, you will more likely want to submit a batch job, which is described later.

The following flags are mandatory for invoking AlphaFold:

• --fasta_paths specifies the location of your fasta files (this cannot be a directory, but it can be a comma-separated list of full paths.

• --max_template_date specifies the latest date to reference when matching against templates. As of 2.2.0, there is no way to “turn off” templates - you can simply provide a very early date to make sure no templates survive the date filter, e.g. --max_template_date=1950-01-01 .

• --output_dir specifies the directory where your output will be written to.

The --data_dir flag is not mandatory, but it will point to /n/shared_db/alphafold by default, where RC has centrally downloaded the databases. If you would rather use your own (not recommended due to requiring approximately 2T of free space), feel free to set this flag with the corresponding location.

You can invoke alphafold.py -h for more information about these, and other optional flags and their options.

The following is an example invocation of alphafold.py with a placeholder output path, including the module load step:

$ module load alphafold/2.2.0

alphafold.py --fasta_paths=/path/to/fastafile --max_template_date=2020-05-14 --db_preset=full_dbs --output_dir=/path/to/output --data_dir=/n/shared_db/alphafold/ 

Example Submission Template

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