mkdir clean
paste <(ls --quote-name ./qc/sg_*_R1_val_1.fq.gz) <(ls --quote-name ./qc/sg_*_R2_val_2.fq.gz) |sed 's/"./-1 ./' | sed 's/gz"\t/gz\t -2 /' | sed 's/"//g' |\
      while read args ; do
                           bowtie2  -x ./MrBean_genome_final/dl_mt -p 4 -k 1 -N 1 -L 25 $args --un-conc-gz ./clean/{$args | sed -e 's/.fq.gz.*$//' -e 's/-1 .\/qc\///' -e 's/_R1_val_1//' }.gz -S a.sam

done

 paste <(ls --quote-name ./qc/sg_*_R1_val_1.fq.gz) <(ls --quote-name ./qc/sg_*_R2_val_2.fq.gz) |sed 's/"./-1 ./' | sed 's/gz"\t/gz\t -2 /' | sed 's/"//g'
-1 ./qc/sg_21_L001_R1_val_1.fq.gz        -2 ./qc/sg_21_L001_R2_val_2.fq.gz
-1 ./qc/sg_21_L002_R1_val_1.fq.gz        -2 ./qc/sg_21_L002_R2_val_2.fq.gz
-1 ./qc/sg_22_L001_R1_val_1.fq.gz        -2 ./qc/sg_22_L001_R2_val_2.fq.gz
-1 ./qc/sg_22_L002_R1_val_1.fq.gz        -2 ./qc/sg_22_L002_R2_val_2.fq.gz
-1 ./qc/sg_23_L001_R1_val_1.fq.gz        -2 ./qc/sg_23_L001_R2_val_2.fq.gz
-1 ./qc/sg_23_L002_R1_val_1.fq.gz        -2 ./qc/sg_23_L002_R2_val_2.fq.gz
-1 ./qc/sg_25_L001_R1_val_1.fq.gz        -2 ./qc/sg_25_L001_R2_val_2.fq.gz

--un-conc-gz ./clean/{$args | sed -e 's/.fq.gz.*$//' -e 's/-1 .\/qc\///' -e 's/_R1_val_1//' }.gz

sg_21_L001
sg_21_L002
sg_22_L001
sg_22_L002
sg_23_L001
sg_23_L002
sg_25_L001

--un-conc-gz ./clean/{echo "$args" | sed 's/.fq.gz.*$//' |sed 's/-1 .\/qc\///' |sed 's/_R1_val_1//'}.gz