Sam’s Notebook: Transcriptome Annotation – C.bairdi Trinity Assembly BLASTx on Mox

In preparation for complete transcriptome annotation of the C.bairdi de novo assembly fro 20191218, I needed to run BLASTx. The assembly was BLASTed against the SwissProt database that comes with Trinotate

SBATCH script (GitHub):

#!/bin/bash ## Job Name #SBATCH --job-name=blastx_cbai ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=25-00:00:00 ## 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 --chdir=/gscratch/scrubbed/samwhite/outputs/20191224_cbai_blastx_outfmt-11 # Load Python Mox module for Python module availability module load intel-python3_2017 # Document programs in PATH (primarily for program version ID) { date echo "" echo "System PATH for $SLURM_JOB_ID" echo "" printf "%0.s-" {1..10} echo "${PATH}" | tr : \\n } >> system_path.log wd="$(pwd)" timestamp=$(date +%Y%m%d) # Paths to input/output files blastx_out="${wd}/${timestamp}-20191218.C_bairdi.Trinity.fasta.blastx.asn" sp_db="/gscratch/srlab/programs/Trinotate-v3.1.1/admin/uniprot_sprot.pep" trinity_fasta="/gscratch/scrubbed/samwhite/outputs/20191218_cbai_trinity_RNAseq/trinity_out_dir/20191218.C_bairdi.Trinity.fasta" # Paths to programs blast_dir="/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin" blastx="${blast_dir}/blastx" threads=28 # Run blastx on Trinity fasta "${blastx}" \ -query "${trinity_fasta}" \ -db "${sp_db}" \ -max_target_seqs 1 \ -outfmt 11 \ -evalue 1e-4 \ -num_threads "${threads}" \ > "${blastx_out}"