---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Annotation - Olurida_v081 MAKER ID Mapping
date: '2019-01-08 07:44'
tags:
  - MAKER
  - Ostrea lurida
  - Olympia oyster
  - mox
categories:
  - 2019
  - Olympia Oyster Genome Sequencing
---
[After getting through the initial MAKER annotation and SNAP gene predictions](https://robertslab.github.io/sams-notebook/posts/2018/2018-11-27-Annotation---Olurida_v081-MAKER-on-Mox/), I needed (wanted?) to simplify annotation names that will be easier to read and are in a more standardized format; similiar to NCBI.

MAKER provides this functionality.

Ran the following SBATCH script on Mox:

- [20190108_oly_maker_id_mapping/20190108_oly_maker_id_mapping.sh](https://gannet.fish.washington.edu/Atumefaciens/20190108_oly_maker_id_mapping/20190108_oly_maker_id_mapping.sh) (text file)

<pre><code>
#!/bin/bash
## Job Name
#SBATCH --job-name=maker
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=15-00:00:00
## Memory per node
#SBATCH --mem=120G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/scrubbed/samwhite/outputs/20190108_oly_maker_id_mapping

# Load Python Mox module for Python module availability

module load intel-python3_2017

# Load Open MPI module for parallel, multi-node processing

module load icc_19-ompi_3.1.2

# SegFault fix?
export THREADS_DAEMON_MODEL=1

# Document programs in PATH (primarily for program version ID)

date >> system_path.log
echo "" >> system_path.log
echo "System PATH for $SLURM_JOB_ID" >> system_path.log
echo "" >> system_path.log
printf "%0.s-" {1..10} >> system_path.log
echo ${PATH} | tr : \\n >> system_path.log

# Variables
maker_dir=/gscratch/srlab/programs/maker-2.31.10/bin

maker_prot_fasta=/gscratch/scrubbed/samwhite/outputs/20181127_oly_maker_genome_annotation/snap02/20181127_oly_genome_snap02.all.maker.proteins.fasta
maker_transcripts_fasta=/gscratch/scrubbed/samwhite/outputs/20181127_oly_maker_genome_annotation/snap02/20181127_oly_genome_snap02.all.maker.transcripts.fasta
snap02_gff=/gscratch/scrubbed/samwhite/outputs/20181127_oly_maker_genome_annotation/snap02/20181127_oly_genome_snap02.all.gff

cp ${maker_prot_fasta} 20181127_oly_genome_snap02.all.maker.proteins.renamed.fasta
cp ${maker_transcripts_fasta} 20181127_oly_genome_snap02.all.maker.transcripts.renamed.fasta
cp ${snap02_gff} 20181127_oly_genome_snap02.all.renamed.gff

# Run MAKER programs
## Change gene names
${maker_dir}/maker_map_ids \
--prefix OLUR_ \
--justify 8 \
${snap02_gff} \
> 20181127_oly_genome.map

## Map GFF IDs
${maker_dir}/map_gff_ids \
20181127_oly_genome.map \
20181127_oly_genome_snap02.all.renamed.gff

## Map FastAs
### Proteins
${maker_dir}/map_fasta_ids \
20181127_oly_genome.map \
20181127_oly_genome_snap02.all.maker.proteins.renamed.fasta

### Transcripts
${maker_dir}/map_fasta_ids \
20181127_oly_genome.map \
20181127_oly_genome_snap02.all.maker.transcripts.renamed.fasta
</code></pre>

---

# RESULTS

Output folder:

- [20190108_oly_maker_id_mapping/](https://gannet.fish.washington.edu/Atumefaciens/20190108_oly_maker_id_mapping/)

Mapping file (text):

- [20190108_oly_maker_id_mapping/20181127_oly_genome.map](https://gannet.fish.washington.edu/Atumefaciens/20190108_oly_maker_id_mapping/20181127_oly_genome.map) (2.7MB)

Renamed GFF:

- [20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.renamed.gff](https://gannet.fish.washington.edu/Atumefaciens/20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.renamed.gff) (2.3GB)

Renamed protein FastA:

- [20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.maker.proteins.renamed.fasta](https://gannet.fish.washington.edu/Atumefaciens/20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.maker.proteins.renamed.fasta) (10MB)

Renamed transcripts FastA:

- [20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.maker.transcripts.renamed.fasta](https://gannet.fish.washington.edu/Atumefaciens/20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.maker.transcripts.renamed.fasta) (30MB)



Here's a look at the files to show that this worked.

---

- Map file

###### This files is used as a key for the name conversions, original names on left, new names on right

![head map file](https://raw.githubusercontent.com/RobertsLab/sams-notebook/master/images/screencaps/20190108_001.png)

---

- Proteins FastA

###### Note the name update at the beginning of the FastA descriptions: ```Olurida_#########-RA```

![head proteins FastA](https://raw.githubusercontent.com/RobertsLab/sams-notebook/master/images/screencaps/20190108_002.png)

---

- Transcripts FastA

###### Note the name update at the beginning of the FastA descriptions: ```Olurida_#########-RA```

![head transcripts FastA](https://raw.githubusercontent.com/RobertsLab/sams-notebook/master/images/screencaps/20190108_003.png)

---

- GFF

###### The new IDs are present but only shown for gene models:

![head GFF](https://raw.githubusercontent.com/RobertsLab/sams-notebook/master/images/screencaps/20190108_004.png)


![gene models GFF](https://raw.githubusercontent.com/RobertsLab/sams-notebook/master/images/screencaps/20190108_005.png)

Regardless, the next steps are to use the newly labeled protein FastA file for BLASTp and protein domain identification. Will move forward with those two steps.