If you have strains with missing data then you must give them the value ?. For example, if you are running a reconstruction of country and you don't know the country for a particular strain, you must set country to ? in the metadata file for that strain. Note that anything else -- empty strings, NA, unknown-- will be interpretted as a valid value!
Currently there is no way to not infer the value of these missing data, but we are working on making this option available in the future.