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.