Annotation - Olurida_v081 MAKER Functional Annotations on Mox

2019
Olympia Oyster Genome Sequencing
Author

Sam White

Published

January 9, 2019

Believe it or not, full, proper annotation of the Olympia oyster genome is nearly complete! Here’s where it stands:

I ran the following SBATCH script on Mox to tackle that last item:


#!/bin/bash
## Job Name
#SBATCH --job-name=maker
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## 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/20190109_oly_maker_functional_annotation

# 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/20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.maker.proteins.renamed.fasta
maker_put_prot_fasta=20181127_oly_genome_snap02.all.maker.proteins.renamed.putative_function.fasta
maker_transcripts_fasta=/gscratch/scrubbed/samwhite/outputs/20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.maker.transcripts.renamed.fasta
maker_put_transcripts_fasta=20181127_oly_genome_snap02.all.maker.transcripts.renamed.putative_function.fasta
snap02_gff=/gscratch/scrubbed/samwhite/outputs/20190108_oly_maker_id_mapping/20181127_oly_genome_snap02.all.renamed.gff
snap02_put_gff=20181127_oly_genome_snap02.all.renamed.putative_function.gff
snap02_put_domains_gff=20181127_oly_genome_snap02.all.renamed.putative_function.domain_added.gff
snap02_put_domains_visible_gff=20181127_oly_genome_snap02.all.renamed.visible_ips_domains.gff
blastp_out=/gscratch/scrubbed/samwhite/outputs/20190108_oly_maker_blastp/20190108_blastp.outfmt6
maker_ips=/gscratch/scrubbed/samwhite/outputs/20190108_oly_maker_interproscan/20190108_oly_maker_proteins_ips.tsv
sp_db=/gscratch/srlab/blastdbs/UniProtKB_20190109/uniprot_sprot.fasta



## Add putative gene functions
### GFF
${maker_dir}/maker_functional_gff \
${sp_db} \
${blastp_out} \
${snap02_gff} \
> ${snap02_put_gff}

### Proteins
${maker_dir}/maker_functional_fasta \
${sp_db} \
${blastp_out} \
${maker_prot_fasta} \
> ${maker_put_prot_fasta}

### Transcripts
${maker_dir}/maker_functional_fasta \
${sp_db} \
${blastp_out} \
${maker_transcripts_fasta} \
> ${maker_put_transcripts_fasta}

## Add InterProScan domain info
### Add searchable tags
${maker_dir}/ipr_update_gff \
${snap02_put_gff} \
${maker_ips} \
> ${snap02_put_domains_gff}

### Add viewable features for genome browsers (JBrowse, Gbrowse, Web Apollo)
${maker_dir}/iprscan2gff3 \
${maker_ips} \
${snap02_gff} \
> ${snap02_put_domains_visible_gff}

RESULTS

Awesome!!! I can’t believe this is actually complete!!! It’s been a long, long road.

A quick summary of the big picture results:

  • 139671 coding sequences

  • 142530 exons

  • 9468 5’ UTRs

  • 24680 genes

  • 24680 mRNAs

  • 6598 3’ UTRs

Next, I’d like to evaluate the genome using BUSCO, as well as run a final gene training/modeling with Augustus.

Output folder:

GFF (2.3GB):

Proteins FastA (12MB):

Transcripts FastA (32MB):