index: preparing for a real run
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
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).
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.