I apologize for using code notation with my file content, but the formatting was weird otherwise.

I have a line file 6,6494,940 containing the following:

@MSQ-M01247R:81:000000000-ACWD8:1:1101:11811:1088 2:N:0:
CCCCCTCTTCCCTTTCTTCCCCCCTCTTTCTTCTTTCTCTTTTCTCCCTCTCCTTTTTTTCTCCTTTTTTTCCTTT
+
############################################################################

      

        
        
        
      

    

I want to write the first 10 characters of each line to a new file in order:

@MSQ-M0124
CCCCCTCTTC
+
##########

      

        
        
        
      

    

I used the following bash script:

while read line
do
        long=$line
        short=${long:0:10}
        echo ${short} 
done < $1

      

        
        
        
      

    

With the following command:

./bashscript.sh fileread.fastq >> filewrite.fastq

      

        
        
        
      

    

results

Something went wrong. My new / write file had 628,429,568 but it should have had 66,494,940, just like the original / read file. So it looks like it was continuing the cycle.

When I use the head command on the new / write file, I get:

@MSQ-M0124
CCCCCTCTTC
+
##########
@MSQ-M0124
CCTCCTCCTT
+
##########
@MSQ-M0124
CCTTCTTCTT

      

        
        
        
      

    

When I use the tail command, I get:

CCCCCGGGGG
+
CCCCCGGGGG
GAGTCGTCTG
+
CCCCCGGGGG
+
CCCCCGGGGG
GAGTCGTCTG
+
CCCCCGGGGG
+
CCCCCGGGGG
GAGTCGTCTG
+