Hello I have a pb On running input_dir="$HOME/workdir/group" output_dir="$HOME/workdir/group/fqdata_trimmed" adap="$CONDA_PREFIX/share/trimmomatic-0.39-1/adapters" f1="$HOME/workdir/group/P4.R1.fq.gz" f2="$HOME/workdir/group/P4.R2.fq.gz" newf1="$HOME/workdir/group/P4.R1.pe.trim.fq.gz" newf2="$HOME/workdir/group/P4.R2.pe.trim.fq.gz" newf1u="$HOME/workdir/group/P4.R1.se.trim.fq.gz" newf2u="$HOME/workdir/group/P4.R2.se.trim.fq.gz"
mismatch_values=(1 2 3 4 5)
for mismatch_value in "${mismatch_values[@]}" do trimmomatic PE -threads 1 -phred33 -trimlog trimLogFile -summary statsSummaryFile \ $f1 $f2 $newf1 $newf1U $newf2 $newf2U \ ILLUMINACLIP:$adap/TruSeq3-PE-2.fa:${mismatch_value}:30:10:1 \ SLIDINGWINDOW:4:15 MINLEN:36 done
I got