shell11

content = $1
for i in `ls -d *`
do
    echo -e "zcat "$i"_S1_L1_R2_001.fastq.gz >"$i"_S1_L1_R2_001.fastq" >./$i/$i.sh
    echo -e "python train.py "$i"_S1_L1_R2_001.fastq outfile.txt " ${content}>>./$i/$i.sh
done

ls ./*/*sh | grep -v run | awk -F "/" '{print "cd "$2 " && qsub -V -cwd -q  -l vf=4g "$3" && cd .."}' | sh