We discovered an issue in QIIME 1.9.0 with alignment of 16S amplicons that are generated with non-515F/806R primers when using PyNAST with the default template alignment. This bug will only be a problem for your analysis if it meets those exact criteria.
This bug stems from an issue with the template alignment that is packaged in the qiime-default-reference project, and would cause many of your sequences to fail to align with PyNAST. The issue is discussed in more detail, including a description of a work-around that we’re currently testing, on qiime-default-reference issue #14. Please follow that issue to track progress on this. We’ll follow-up on the blog and QIIME forum when a fix is ready – we expect that this will be this week.
We know that this is very inconvenient, and we apologize for any issues this may have caused. If you have any questions about this, please don’t hesitate to follow up on the forum. If you’d like to know if this issue affected one of your runs, please post to the forum with the output of running print_qiime_config.py.