Genome Annotation on Galaxea fasicularis

Map KEGG terms to genome

This post is inspired by E. Chille’s, D. Becker’s and my post on genomic functional annotations.

1. Download and inflate the Kofam database

Already completed in this post

2. Run KofamScan

Download Gfas protein file:

wget http://gfas.reefgenomics.org/download/gfas_1.0.proteins.fasta.gz
gunzip gfas_1.0.proteins.fasta.gz 

nano kofamscan_gfas.sh

#!/bin/bash
#SBATCH --job-name="KofamScan"
#SBATCH -t 30-00:00:00
#SBATCH --export=NONE
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=kevin_wong1@uri.edu
#SBATCH --nodes=1 --ntasks-per-node=20
#SBATCH --mem=100GB
#SBATCH -D /data/putnamlab/kevin_wong1/kofamscan

echo "Loading modules" $(date)
module load kofam_scan/1.3.0-foss-2019b
module load libyaml/0.1.5
module unload HMMER/3.3.1-foss-2019b
module load HMMER/3.3.2-gompi-2019b
module list

#echo "Starting analysis... downloading KO database" $(date)
#wget ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz #download KO database
#wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz
#gunzip ko_list.gz
#tar xf profiles.tar.gz

echo "Beginning mapping" $(date)
/opt/software/kofam_scan/1.3.0-foss-2019b/exec_annotation \
-o Gfas_KO_annot.txt \
-k ./ko_list \
-p ./profiles/eukaryote.hal \
-E 0.00001 \
-f detail-tsv \
--report-unannotated ./gfas_1.0.proteins.fasta

echo "Analysis complete!" $(date)

scp -r kevin_wong1@ssh3.hac.uri.edu:/data/putnamlab/kevin_wong1/kofamscan/Gfas_KO_annot.txt /Users/kevinwong/MyProjects/DarkGenes_Bleaching_Comparison/output/Annotations/Gfas_KO_annot.txt

InterProScan

Resources:

nano interproscan_gfas.sh

#!/bin/bash
#SBATCH --job-name="InterProScan"
#SBATCH -t 30-00:00:00
#SBATCH --export=NONE
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=kevin_wong1@uri.edu
#SBATCH --mem=100GB
#SBATCH --error="interproscan_out_error"
#SBATCH --output="interproscan_out"
#SBATCH -D /data/putnamlab/kevin_wong1/interproscan

echo "START $(date)"

# Load module
module load InterProScan/5.60-92.0-foss-2021b
module load Java/11.0.2
java -version

interproscan.sh --cpu $SLURM_CPUS_ON_NODE ...
interproscan.sh -version
interproscan.sh -f TSV -i gfas_1.0.proteins.fasta -b Gfas.interpro.20231004 -iprlookup -goterms -pa
#interproscan.sh -mode convert -f GFF3 -i Past.interpro.20220113.xml -b Past.interpro.20220113

# -i is the input data
# -b is the output file base
# -f is formats
# -iprlookup enables mapping
# -goterms is GO Term
# -pa is pathway mapping
# -version displays version number

echo "DONE $(date)"

eggNOG-Mapper

http://eggnog-mapper.embl.de/

used the metazoan and all database and default parameters.

Written on September 11, 2023