---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: RepeatModeler - Pgenerosa_v074 for MAKER Annotation on Emu
date: '2019-06-26 12:09'
tags:
  - repeatmodeler
  - Panopea generosa
  - geoduck
  - jupyter
  - roadrunner
  - v074
categories:
  - 2019
  - Miscellaneous
---
[Yesterday (20190625)](https://robertslab.github.io/sams-notebook/posts/2019/2019-06-25-Data-Wrangling---FastA-Subsetting-of-Pgenerosa_v070.fa-Using-samtools-faidx/) I generated a subset of the first 18 FastA sequences from the [Pgenerosa_v070.fa](http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v070.fa) file. This subset has been designated as Pgenerosa_v074 by Steven. It's available on our Genomic Resources wiki:

- [Pgenerosa_v074.fa](http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v074.fa)

He's asked me to annotate this assembly using MAKER - this will be detailed in another notebook entry at some point.

In preparation for that, I need to run the assembly through RepeatModeler and provide the output to MAKER. I ran RepeatModeler v1.0.11 on Emu (Apple Xserve running Ubuntu 16.04LTS).

All of it is detailed in this Jupyter Notebook (GitHub):

- [20190626_emu_Pgenerosa_v074_repeatmodeler.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190626_emu_Pgenerosa_v074_repeatmodeler.ipynb)

---

# RESULTS

Run time was 1974 minutes (~32.4hrs).

Output folder:

- [20190626_Pgenerosa_v074_repeatmodeler](https://gannet.fish.washington.edu/Atumefaciens/20190626_Pgenerosa_v074_repeatmodeler)


RepeatModeler FastA:

- [20190626_Pgenerosa_v074_repeatmodeler/Pgenerosa_v074-families.fa](https://gannet.fish.washington.edu/Atumefaciens/20190626_Pgenerosa_v074_repeatmodeler/Pgenerosa_v074-families.fa)
