bowtie2_alignment.sh

#!/bin/bash

#SBATCH --job-name=bowtie2_alignment
#SBATCH --output=bowtie2_alignment.out
#SBATCH --error=bowtie2_alignment.err
#SBATCH --time=48:00:00
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=8
#SBATCH --mem-per-cpu=8G

# Load necessary modules
module load StdEnv/2020
module load bowtie2/2.5.1
module load samtools/1.17

# Base directory for SRA data
SRA_DIR="/scratch/a252chan"

# Loop through each SRA ID directory
for SRA_ID_DIR in $SRA_DIR/*/; do
    # Extract the SRA ID from the directory name
    SRA_ID=$(basename $SRA_ID_DIR)

     # Specify the path to the trimmed FASTQ files
    FASTQ_PATH="${SRA_ID_DIR}fastq"

    # Define BAM file path
    BAM_FILE="${SRA_ID_DIR}aligned_${SRA_ID}_reads.bam"

    # Check if trimmed FASTQ files exist
    if [[ -f "${FASTQ_PATH}/trimmed_${SRA_ID}_1.fastq" && -f "${FASTQ_PATH}/trimmed_${SRA_ID}_2.fastq" ]]; then

        # Check if the BAM file exists (from previous runs)
        if [[ -f "$BAM_FILE" ]]; then
            # Check for EOF marker in BAM file
            if samtools quickcheck "$BAM_FILE"; then
                echo "BAM file for $SRA_ID is complete, skipping."
                continue
            else
                echo "BAM file for $SRA_ID is corrupted or incomplete, rerunning alignment."
                
                # Align reads using Bowtie2
                bowtie2 -x /scratch/a252chan/closDifficile/FN545816 \
                -1 "${FASTQ_PATH}/trimmed_${SRA_ID}_1.fastq" \
                -2 "${FASTQ_PATH}/trimmed_${SRA_ID}_2.fastq" \
                | samtools view -bS - > "${SRA_ID_DIR}aligned_${SRA_ID}_reads.bam"
            fi
        else
            echo "BAM file for $SRA_ID not found, starting alignment."
            
            # Align reads using Bowtie2
            bowtie2 -x /scratch/a252chan/closDifficile/FN545816 \
            -1 "${FASTQ_PATH}/trimmed_${SRA_ID}_1.fastq" \
            -2 "${FASTQ_PATH}/trimmed_${SRA_ID}_2.fastq" \
            | samtools view -bS - > "${SRA_ID_DIR}aligned_${SRA_ID}_reads.bam"
        fi

        # Remove untrimmed FASTQ files
        find "${FASTQ_PATH}" -type f -name '*.fastq' ! -name '*trimmed*' -exec rm {} +
    else
        echo "Trimmed FASTQ files for $SRA_ID not found."
    fi
done