fetch and index: preparing for a real run

Fetching databases

After installation, one needs to populate the database directory. By default this will be /data/virmet_databases and will occupy about 60 GB. In order to populate this, use the subcommand fetch, for example as follows

virmet fetch --viral n  # this downloads viral sequences, nucleotide only
virmet fetch --human
virmet fetch --bact
virmet fetch --fungal
virmet fetch --bovine

This might take long. If it's taking too long, you might want to include the above commands in a down.sh file and run them overnight.

Only the option --viral takes an argument: n for nucleotide and p for protein viral database. Currently only nucleotide sequences are used, while the protein ones are foreseen as useful in discovery of novel viral sequences (in a future version).

Indexing databases

The subcommand virmet index can take multiple arguments, so you can run

virmet index --viral n --human --bact --fungal --bovine

and wait for the indexing to finish.