Update: There is now an updated version of Metaxa2 that addresses this problem. Find it here.
We have recently discovered that the new version of HMMER (3.3) released in November 2019 have introduced new restrictions that make it partially incompatible with Metaxa2. The most apparent problem is in the Database Builder software, which will not build profiles properly in most cases. Instead, HMMER will return an error and only some profiles will be created.
We do currently not know if this also affects the functionality of Metaxa2 itself. We are currently investigating this.
For now, the solution to this problem is to use the previous version of HMMER (version 3.2.1) while we investigate further. That version can be downloaded here: http://hmmer.org/download.html
I am sorry about not discovering this earlier, this only came to our attention this week!