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_heart
## 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_heart_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="${wd}/blastx.outfmt6"
sp_db="/gscratch/srlab/programs/Trinotate-v3.1.1/admin/uniprot_sprot.pep"
trinity_fasta="/gscratch/scrubbed/samwhite/outputs/20190215_trinity_geoduck_heart_RNAseq/trinity_out_dir/Trinity.fasta"
# Paths to programs
blast_dir="/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin"
blastx="${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}
RESULTS
Output folder:
BLASTx output (output format 6):