Sam’s Notebook: Annotation – Olurida_v081 MAKER Proteins BLASTp on Mox

After getting through the initial MAKER annotation and SNAP gene predictions, I needed to run BLASTp on the FastA file produced by MAKER in order to assign some functionality to the predicted genes.

Input FastA (9.3MB):

SBATCH script (text file):

  #!/bin/bash ## Job Name #SBATCH --job-name=blastp ## 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/20181220_oly_maker_blastp # 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 # 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 ${PATH} | tr : \\n >> system_path.log # Add BLAST to system PATH export PATH=$PATH:/gscratch/srlab/programs/ncbi-blast-2.6.0+/bin export BLASTDB=/gscratch/srlab/blastdbs/UniProtKB_20181008/ # Define variables blastp=/gscratch/srlab/programs/ncbi-blast-2.6.0+/bin/blastp uniprot_db=/gscratch/srlab/blastdbs/UniProtKB_20181008/20181008_uniprot_sprot.fasta maker_p_fasta=/gscratch/scrubbed/samwhite/outputs/20181127_oly_maker_genome_annotation/Olurida_v081.all.maker.proteins.fasta output=/gscratch/scrubbed/samwhite/outputs/20181220_oly_maker_blastp/20181220_outfmt6.blastp # Run blastp ${blastp} \ -query ${maker_p_fasta} \ -db ${uniprot_db} \ -out ${output} \ -max_target_seqs 1 \ -evalue 1e-6 \ -outfmt 6 \ -num_threads 28