---
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)

<iframe src="https://render.githubusercontent.com/view/ipynb?commit=a3ef85c9bcdfed486290e2ae383c75a6ab64d3f4&enc_url=68747470733a2f2f7261772e67697468756275736572636f6e74656e742e636f6d2f73723332302f4c6162446f63732f613365663835633962636466656434383632393065326165333833633735613661623634643366342f6a7570797465725f6e62732f73616d2f32303136303432385f4f6c795f4742535f535441434b532e6970796e62&nwo=sr320%2FLabDocs&path=jupyter_nbs%2Fsam%2F20160428_Oly_GBS_STACKS.ipynb&repository_id=13746500#7e520a80-01bf-44d1-b373-e3606e0f6564" width="100%" height="2000" scrolling="yes"></iframe>