Sam’s Notebook: Transcriptome Annotation – Geoduck Ctenidia with BLASTx on Mox

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx on Mox.

SBATCH script:

  #!/bin/bash ## Job Name #SBATCH --job-name=blastx_ctendia ## 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 --workdir=/gscratch/scrubbed/samwhite/outputs/20190318_blastx_geoduck_ctenidia_RNAseq # Load Python Mox module for Python module availability module load intel-python3_2017 # 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 ${PATH} | tr : \\n >> system_path.log wd="$(pwd)" # Paths to input/output files blastx_out="${wd}/blastx.outfmt6" sp_db="/gscratch/srlab/programs/Trinotate-v3.1.1/admin/uniprot_sprot.pep" trinity_fasta="/gscratch/scrubbed/samwhite/outputs/20190215_trinity_geoduck_ctenidia_RNAseq/trinity_out_dir/Trinity.fasta" # Paths to programs blast_dir="/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin" blastx="${blast_dir}/blastx" # Run blastx on Trinity fasta ${blastx} \ -query ${trinity_fasta} \ -db ${sp_db} \ -max_target_seqs 1 \ -outfmt 6 \ -evalue 1e-3 \ -num_threads 28 \ > ${blastx_out}