Sam’s Notebook: Annotation – Olurida_v081 MAKER ID Mapping

After getting through the initial MAKER annotation and SNAP gene predictions, 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:

  #!/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