No word from the QIIME forum about my problem. So, I asked twitter for help.

So far, everyone thinks it has something to do with my path, BUT 1) macqiime sets the PYTHONPATH variable, and 2) the package it’s looking for exists in both macqiime python and anaconda.

OK, so it’s fixed now. There may be another way to deal with it, but what I did was install ipython notebook into the macqiime python folder, using get-pip.py to install pip, and then pip install ipython[notebook], and then comment out the line in my .bash_profile that points to the anaconda version of ipython.

Marisano James actually did all of the work for me, I asked him to summarize:

“When anaconda was installed, it added a path to its own ipython in the .bash_profile. Then, no matter what python was running, it would wind up using the anaconda version of ipython, which didn’t have the same settings as the system Python. I wound up renaming the anaconda folder (so it could no longer be found), and then commenting out the added line in ~/.bash_profile. Just commenting out the line in the ~/.bash_profile is sufficient, but I didn’t know anaconda’s ipython was being called until I effectively removed its folder. If you run into this problem, be sure to open a new terminal after commenting out the offending anaconda ipython line so it will be able to use the updated PATH.”