If I run metaphlan 3.0.7 with no internet connection, but try to provide a local copy of the database via
--bowtie2db $DBDIR, I get the warning:
WARNING: It seems that you do not have Internet access. WARNING: Cannot connect to the database server. The latest available local database will be used.
…and the bugs output files are all empty for all samples, but when I use an internet connection with the same metaphlan command, the bugs files are filled with taxonomic information.
It appears that metaphlan 3.0.7 is not actually defaulting to a local database if no internet connection; it instead just using nothing and does not warn the user or die.
Also, how is one supposed to properly provide a local database? I thought that it was
--bowtie2db $DBDIR, but that doesn’t seem to do it.
Installing the databases within the metaphlan install directory is an option that I want to avoid, given that software install locations are not meant for large database files, and that option precludes the possibility of sharing the same database with many users and/or metaphlan installs, which results in a lot of redundant database downloading and storage.