We have now added a bug fix for qiime-default-reference issue #14, which is the bug mentioned in my most recent blog post. If you’ve install QIIME with pip, or are working in the AWS instance or QIIME VirtualBox, you can fix this bug by running:
pip install --upgrade qiime-default-reference
You may need to preface this command with sudo, depending on how you installed QIIME. For example:
sudo pip install --upgrade qiime-default-reference
This will update the default template alignment used by PyNAST to be the PyNAST-aligned (rather than SSU-aligned) Greengenes 13_8 85% OTU representative sequences.
To confirm that the update was successful, you should run print_qiime_config.py. This should list the version of qiime-default-reference as 0.1.2. For example:
Comparisons of PyNAST aligning against both the Greengenes core set (as used in QIIME 1.8.0 and earlier) and the PyNAST-aligned Greengenes 13_8 85% OTU representative sequences (packaged in qiime-default-reference 0.1.2) are available linked from here.
Again, apologies for any inconvenience this may have caused.