paired end trimming

#!/bin/bash -x
#PBS -N trimmomatics_job
#PBS -q batch
#PBS -l walltime=72:00:00
#PBS -l nodes=1:ppn=4,mem=40gb
#PBS -W x=naccesspolicy:UNIQUEUSER
#PBS -j oe
#PBS -A your_job

module load java
cd /home/pathtoTrimmomatic

INPATH=/home/infiles
OUTPATH=/home/outfiles
mkdir -p $OUTPATH


for file in $INPATH/*.fq.gz
do
        bname=$(basename $file '_1.fq.gz')
        echo "file: "$file
        echo $bname
        input1=$INPATH/$bname"_1.fq.gz"
        input2=$INPATH/$bname"_2.fq.gz"
        output1=$OUTPATH/$bname"_1.paired.fq.gz"
        output2=$OUTPATH/$bname"_1.unpaired.fq.gz"
        output3=$OUTPATH/$bname"_2.paired.fq.gz"
        output4=$OUTPATH/$bname"_2.unpaired.fq.gz"
        echo $input1 $input2
        java -jar trimmomatic-0.39.jar PE  -phred33 \
            "$input1" "$input2" "$output1" "$output2" "$output3" "$output4" \
            ILLUMINACLIP:BGI_Adapters.fa:2:30:10 \
            LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
done