Sam’s Notebook: Transcriptome Annotation – Hematodinium MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

As part of annotating the 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 today) 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/20200123_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/20200122.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