Trouble if a directory exists

Question

I've got the following code:

#!/bin/bash

while read line
do
echo "line" $line
if [[ -d ../Results/${line}_Forward && -d ../Results/${line}_Reverse ]]
then

        cd ../Results/COMBI
        mkdir ./${line}_COMBI
        cd ..
        for (( win = 2; win < 20; win += 2 )); do
        printf 'The value of win is %d, now entereing inner loop\n' "$win"

        for (( per = 50; per < 100; per += 2 )); do
            printf 'Value of per is %d\n' "$per"
            merger -asequence ./${line}_Forward/${line}_Forward_Trimmed_w${win}_p${per}.fa -bsequence ./${line}_Reverse/REV_COMP/${line}_Reverse_Trimmed_w${win}_p${per}_RevComp.fa -outseq ./COMBI/${line}_COMBI/${line}_w${win}_p${per}_COMBI.fa
        done
        done
else
    echo $line "Forward or Reverse directory does not exist"
fi
done < ./Data_ORD.txt

When i run the script any dictory contained in the if statment exits but they actually do. And i get this kind of output for each line in Data_ORD.txt:

line  ORD0926
 Forward or Reverse directory does not exist

in the last echo $line variable is not printed. I guess something is wrong with this variable but or with the if statement.

Any idea's why $line is not printed in the last echo and directories are not recognized by the if statement?

**.fa: fasta formats which are plain text formats containing DNA sequences. **merger command: contained in the EMBOSS package "The European Molecular Biology Open Software Suite"

Answer 1

Im checking whether if both directories exist. I created a new variable after then which cuts codes contained in the data file: wth=echo ${line} | cut -c 1-7

#!/bin/bash

while read line
do
echo "line" $line
wth=`echo ${line} |  cut -c 1-7`
echo "wth" ${wth}
if [[ -d ../Results/${wth}_Forward && -d ../Results/${wth}_Reverse ]]
then

        cd ../Results/COMBI
        mkdir ./${wth}_COMBI
        cd ..
        for (( win = 2; win < 20; win += 2 )); do
        printf 'The value of win is %d, now entereing inner loop\n' "$win"

        for (( per = 50; per < 100; per += 2 )); do
            printf 'Value of per is %d\n' "$per"
            merger -asequence ./${wth}_Forward/${wth}_Forward_Trimmed_w${win}_p${per}.fa -bsequence ./${wth}_Reverse/REV_COMP/${wth}_Reverse_w${win}_p${per}_RevComp.fa -outfile none -outseq ./COMBI/${wth}_COMBI/${wth}_w${win}_p${per}_COMBI.fa
        done
        done
else
    echo ${wth} "Forward or Reverse directory does not exist"
fi
done < ./Data_ORD.txt

Now the script works. It seems calling directly $line as a variable isn't a good idea since there can be some unseen spaces.