---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2017-03-14 22:56:21+00:00
layout: post
slug: computing-oly-bgi-gbs-reproducibility-fail-but-less-so-than-last-time
title: Computing – Oly BGI GBS Reproducibility Fail (but, less so than last time)...
categories:
  - 2017
  - BS-seq Libraries for Sequencing at Genewiz
tags:
  - BGI
  - iTools
  - jupyter notebook
  - olympia oyster
  - Ostrea lurida
---

Well, [my previous attempt at reproducing the demultiplexing that BGI performed was an exercise in futility](https://robertslab.github.io/sams-notebook/posts/2017/2017-03-07-computing-oly-bgi-gbs-reproducibility-fail/). BGI got back to me with the following message:





<blockquote>Hi Sam,

We downloaded it and it seems fine when compiling. You can compile it with the below command under Linux system.

tar -zxvf ReSeqTools_XXX.tar.gz ; cd iTools_Code; chmod 775 iTools ; ./ iTools -h</blockquote>





I gave that whirl and got the following message:


    
    <code>Error opening terminal: xterm</code>



Some internet searching got me sucked into a useless black hole about 64 bit systems running 32 bit programs and enabling the 64 bit kernel on Mac OS X 10.7.5 (Lion) since it's not enabled by default and on and on. In the end, I can't seem to enable the 64 bit kernel on my Mac Pro, likely due to hardware limitations related to the graphics card and/or displays that are connected.

Anyway, I decided to try getting this program installed again, using a Docker container (instead of trying to install locally on my Mac).



Results:

It didn't work again, but for a different reason! Despite the instructions in the readme file provided with iTools, you don't actually need to run `make`! All that has to be done is unzipping the tarball!! However, despite figuring this out, the program fails with the following error message: "Warming : sample double in this INDEX Files. Sample ID: OYSzenG1AAD96FAAPEI-109; please renamed it diff" (note: this is copied/pasted - the spelling errors are note mine). So, I think there's something wrong with the formatting of the index file that BGI provided me with.

I've contacted them for more info.

See the Jupyter notebook linked below to see what I tried.

Jupyter notebook (GitHub): [20170314_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20170314_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb)
