As part of addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I needed to extract the reads ID’ed via BLASTX against the C.opilio genome on 20210312. Read extractions were performed using SeqKit on Mox.

SBATCH script (GitHub):

• 20210316_cbai-vs-copi_reads_extractions.sh

#!/bin/bash ## Job Name #SBATCH --job-name=20210316_cbai-vs-copi_reads_extractions ## 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 ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20210316_cbai-vs-copi_reads_extractions ## Script for extracting C.bairdi RNAseq reads that matched to C.opilio ## genome via BLASTx on 20210312. ## Inputs are lists of RNAseq IDs ## Outputs are gzipped FastQ files of extracted reads ################################################################################### # These variables need to be set by user threads=40 # FastQ directory reads_dir=/gscratch/srlab/sam/data/C_bairdi/RNAseq # BLASTx results directory blastx_dir=/gscratch/scrubbed/samwhite/outputs/20210312_cbai-vs-copi_diamond_blastx # Programs array declare -A programs_array programs_array=( [seqkit]="/gscratch/srlab/programs/seqkit-0.15.0" \ [seqkit_grep]="/gscratch/srlab/programs/seqkit-0.15.0 grep" ) # FastQ array fastq_array=(${reads_dir}/*fastp-trim*.fq.gz) # BLASTx results files with query (FastQ read ID) only blastx_array=(${blastx_dir}/*.blastx.outfmt6-query) ################################################################################### # 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 file in "${!fastq_array[@]}" do # Remove path from transcriptome using parameter substitution no_path="${fastq_array[$file]##*/}" # Remove extensions from filename no_ext=${no_path%.fq.gz} # Set output filename out_file="${no_ext}_copi-BLASTx-match.fq.gz" # Generate checksums for reference echo "" echo "Generating checksum for ${fastq_array[$file]}." md5sum "${fastq_array[$file]}" >> fastq.checksums.md5 echo "Completed checksum for ${fastq_array[$file]}." echo "" # Extract reads using results from BLASTx files ${programs_array[seqkit_grep]} \ --pattern-file ${blastx_array[$file]} \ ${fastq_array[$file]} \ --out-file ${out_file} \ --threads ${threads} # Generate checksums of extracted reads reference echo "" echo "Generating checksum for ${out_file}." md5sum "${out_file}" >> fastq.checksums.md5 echo "Completed checksum for ${out_file}." echo "" done ################################################################################### # Capture program options echo "Logging program options..." for program in "${!programs_array[@]}" do { echo "Program options for ${program}: " echo "" # Handle blank argument for help menus if [[ "${program}" == "samtools_index" ]] \ || [[ "${program}" == "samtools_sort" ]] \ || [[ "${program}" == "samtools_view" ]] \ || [[ "${program}" == "seqkit" ]] 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 "