DIAMOND BLASTx – C.bairdi RNAseq vs C.opilio Genome Proteins on Mox

We want to generate an additional Tanner crab (Chionoecetes bairdi) transcriptome, per this GitHub issue, to generate an additional C.bairdi transcriptome. This has come about due to the release of the genome of a very closely related crab species, Chionoecetes opilio (Snow crab).

I used DIAMOND BLASTx along with the Snow crab genome protein FastA (8.7MB) from NCBI (Acc: GCA_016584305.1).

NOTE: Since this is geared toward just identifying matching reads, the BLASTx output format will only contain the query ID. There will be one BLASTx output file for each corresponding input FastQ file.

SBATCH script (GitHub):

#!/bin/bash ## Job Name #SBATCH --job-name=20210312_cbai-vs-copi_diamond_blastx ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=20-00:00:00 ## Memory per node #SBATCH --mem=120G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=samwhite ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20210312_cbai-vs-copi_diamond_blastx ## Script for running BLASTx (using DIAMOND) with all of our C.bairdi RNAseq data to-date. ## BLASTx against C.opilio _(snow crab) NCBI protein FastA ## Output will be in standard BLAST output format 6, but only query ID. ## Output will be used to extract just reads with matches to to C.opilio genome, ## for downstream transcriptome assembly ################################################################################### # These variables need to be set by user # FastQ directory reads_dir=/gscratch/srlab/sam/data/C_bairdi/RNAseq # DIAMOND database dmnd=/gscratch/srlab/sam/data/C_opilio/blastdbs/GCA_016584305.1_ASM1658430v1_protein.dmnd # Programs array declare -A programs_array programs_array=( [diamond]="/gscratch/srlab/programs/diamond-0.9.29/diamond" ) # FastQ array fastq_array=(${reads_dir}/*fastp-trim*.fq.gz) ################################################################################### # Exit script if any command fails set -e # Load Python Mox module for Python module availability module load intel-python3_2017 # BLASTx FastQ files for fastq in "${!fastq_array[@]}" do # Remove path from transcriptome using parameter substitution fastq_name="${fastq_array[$fastq]##*/}" # Generate checksums for reference echo "" echo "Generating checksum for ${fastq_array[$fastq]}." md5sum "${fastq_array[$fastq]}">> fastq.checksums.md5 echo "Completed checksum for ${fastq_array[$fastq]}." echo "" # Run DIAMOND with blastx # Output format 6 query only returns a single query ID per match # block-size and index-chunks are computing resource optimatization paraeters ${programs_array[diamond]} blastx \ --db ${dmnd} \ --query "${fastq_array[$fastq]}" \ --out "${fastq_name}".blastx.outfmt6-query \ --outfmt 6 qseqid \ --evalue 1e-4 \ --max-target-seqs 1 \ --max-hsps 1 \ --block-size 15.0 \ --index-chunks 4 done ################################################################################### # Capture program options echo "Logging program options..." for program in "${!programs_array[@]}" do { echo "Program options for ${program}: " echo "" # Handle samtools help menus if [[ "${program}" == "samtools_index" ]] \ || [[ "${program}" == "samtools_sort" ]] \ || [[ "${program}" == "samtools_view" ]] then ${programs_array[$program]} # Handle DIAMOND BLAST menu elif [[ "${program}" == "diamond" ]]; then ${programs_array[$program]} help # Handle NCBI BLASTx menu elif [[ "${program}" == "blastx" ]]; then ${programs_array[$program]} -help fi ${programs_array[$program]} -h echo "" echo "" echo "