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:

20190318_blastx_geoduck_gonad_01_RNAseq.sh


#!/bin/bash
## Job Name
#SBATCH --job-name=blastx_gonad_01
## 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_gonad_01_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_gonad_01_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:

20190318_blastx_geoduck_gonad_01_RNAseq

BLASTx output (output format 6):

20190318_blastx_geoduck_gonad_01_RNAseq/blastx.outfmt6