---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2016-05-23 17:44:27+00:00
layout: post
slug: data-analysis-oly-gbs-data-using-stacks-1-37
title: Data Analysis - Oly GBS Data Using Stacks 1.37
categories:
  - 2016
  - Genotype-by-sequencing at BGI
tags:
  - BGI
  - GBS
  - genotype-by-sequencing
  - ipython notebook
  - jupyter notebook
  - olympia oyster
  - Ostrea lurida
  - stacks
---

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](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20160428_Oly_GBS_STACKS.ipynb)

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