I am running a script on paired end illumina data to run trimmomatic to remove adaptor sequences and low quality reads.

The script is below:

input_dir="/home/reads"
# Define the output directory
output_dir="trimmed"
# Create the output directory if it doesn't exist
mkdir -p "$output_dir"

# Loop through all files in the input directory that match the pattern *_1.fastq.gz
for file1 in "$input_dir"/*_1.fastq.gz; do
    # Extract the base name (two-letter code) from the file name
    base_name=$(basename "$file1" _1.fastq.gz)
    file2="${input_dir}/${base_name}_2.fastq.gz"

    # Check if the corresponding _2.fastq.gz file exists
    if [[ -f "$file2" ]]; then
        # Run the trimmomatic command
        trimmomatic PE "$file1" "$file2" \
            -baseout "${output_dir}/${base_name}.fastq.gz" \
            ILLUMINACLIP:adaptors.fasta:4:30:10 MINLEN:30
    else
        echo "Warning: Corresponding file for $file1 not found. Skipping."
    fi
done

The script runs over several hours on my cluster, but when I check the output files that should contain the reads removed by trimmomatic they are empty. I have also run fastqc on the sequence files before and after trimmomatic, and the html report files are identical. I can see from the fastqc outputs that each file fails for "Adapter Content" and contains a high percentage of Illumina Universal Adapter sequences.

Here is the sequence I am using for the Illumina Universal Adapter

>IlluminaUniversalAdapterNA
AGATCGGAAGAG

Why is trimmomatic not removing any reads?

Why is trimmomatic not removing any reads?

It is not mandatory that your data have extraneous/adapter sequence. If no extraneous sequence is present then no reads will be trimmed/removed. That said check to make sure that you are providing correct adapter sequences and that file is readable/accessible.

Run a pair of files manually to make sure that the job is running correctly with the options you are providing. Check the log files to see if you see anything odd.