Data Analysis - Oly GBS Data Using Stacks 1.37

2016
Genotype-by-sequencing at BGI
BGI
GBS
genotype-by-sequencing
ipython notebook
jupyter notebook
olympia oyster
Ostrea lurida
stacks
Author

Sam White

Published

May 23, 2016

This analysis ran (or, more properly, was attempted) for a couple of weeks and failed a few times. The failures seemed to be linked to the external hard drive I was reading/writing data to. It continually locked up, leading to “Segmentation fault” errors.

We’ve replaced the external with a different one in hopes that it’ll be able to handle the workload. Will be attempting to re-run Stacks with the new external hard drive.

I’m posting the Jupyter notebook here for posterity.

Jupyter notebook: 20160428_Oly_GBS_STACKS.ipynb