Sam’s Notebook: Annotation – Olurida_v081 MAKER Functional Annotations on Mox

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}