In the December 2011 version of MacQIIME (MacQIIME_1.4.0-20111216), there was an error in split_libraries.py. This error was fixed in the SVN code for QIIME, and since it's a big bug I made a fix in MacQIIME as well. If you have MacQIIME version 1.4.0-20111216 installed, you can fix it as follows.
The latest download on this site, MacQIIME_1.4.0a-20120108, already includes this fix. If you have this latest version, you don't need to do anything.
FixSplitLibraries_MacQIIME1.4.0.tgz into your Downloads folder (Do not open it with the Archive Utility graphical tool -- we'll unzip it in the command line).
and untar the file:
tar -xvf FixSplitLibraries_MacQIIME1.4.0.tgz
and cd into the new directory:
That should do it! It just replaced two libraries, and the test script for split_libraries.py.