UPDATE (20160418) : I’m posting this more for posterity, as Stacks continually locked up at both the “ustacks” and “cstacks” stages. These processes would take days to run (on the full 96 samples) and then the processes would become “stuck” (viewed via the top command in OS X).

Have moved on to trying PyRAD in the meantime.

Need to get the GBS from BGI data analyzed.

[Installed Stacks (and its dependencies on Hummingbird earlier today)(2016/04/06/software-install-samtools-0-1-19-and-stacks-1-37.html).

Below is the Jupyter (iPython) notebook I ran to perform this analysis.

Jupyter (iPython) Notebook: 20160406_Oly_GBS_STACKS.ipynb

Jupyter Notebook Viewer: 20160406_Oly_GBS_STACKS