As part of annotating the most recent transcriptome assembly from the MEGAN6 Hematodinium taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.
Ran DIAMOND BLASTx against the UniProt/SwissProt database (downloaded 20200123) on Mox.
SBATCH script (GitHub):
#!/bin/bash
## Job Name
#SBATCH --job-name=hemat_blastx_DIAMOND
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=10-00:00:00
## 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/20200331_hemat_diamond_blastx_megan
# Exit script if any command fails
set -e
# Load Python Mox module for Python module availability
module load intel-python3_2017
# SegFault fix?
export THREADS_DAEMON_MODEL=1
# 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
# Program paths
diamond=/gscratch/srlab/programs/diamond-0.9.29/diamond
# DIAMOND UniProt database
dmnd=/gscratch/srlab/blastdbs/uniprot_sprot_20200123/uniprot_sprot.dmnd
# Trinity assembly (FastA)
fasta=/gscratch/srlab/sam/data/Hematodinium/transcriptomes/20200408.hemat.megan.Trinity.fasta
# Strip leading path and extensions
no_path=$(echo "${fasta##*/}")
no_ext=$(echo "${no_path%.*}")
# Run DIAMOND with blastx
# Output format 6 produces a standard BLAST tab-delimited file
${diamond} blastx \
--db ${dmnd} \
--query "${fasta}" \
--out "${no_ext}".blastx.outfmt6 \
--outfmt 6 \
--evalue 1e-4 \
--max-target-seqs 1 \
--block-size 15.0 \
--index-chunks 4
RESULTS
Completed in 9 seconds!
Output folder:
BLASTx output - BLAST format 6 (tab):
Will proceed with Trinotate.