updated to use QIIME's temp_dir

There were two places where QIIME's ``temp_dir`` wasn't being used:

1. When building the BLAST DB to search against. This is fixed by this pull request. 
2. When calling ``pynast.util.pynast_seqs``. This is partially fixed by this pull request, but also requires PyNAST 1.2.1 or later to actually work (the PyNAST release will be published within the next few days). If using PyNAST 1.2.0, QIIME's ``temp_dir`` will be passed to ``pynast_seqs``, though not actually used (``pynast_seqs`` takes ``**kwargs``, so the parameter can be passed but is just ignored). PyNAST 1.2.1 has been updated to actually use that value. 

This fixes #1114.