The second step of validation is checking the Schematron rules. Fortunately, there is nothing to install. Use is just like the conversions you have already been doing. In the PreTeXt distribution, there are three files related to Schematron in the schema directory. Two of them are meant for developer use, or for the curious. The file you are interested in is pretext-schematron.xsl. This is a stylesheet, unique to PreTeXt, which will carefully analyze your source to find any exceptions that the RELAX-NG schema was not designed to catch. You use the stylesheet like any other,
xsltproc schema/pretext-schematron.xsl ~/books/aota/animals.xml

with suitably adjusted paths, and be sure to provide the -xinclude switch if your source is modularized across multiple files (Section 4.2). No news is good news, but each exception found should provide enough explanation for you to locate, and correct, the problem. These messages are under PreTeXt's control, so please report any that are not helpful enough. That's it—easy.