Here your FILEA file is having the individual ids on the same line. i.e individual Ids are not delimited by a new line. So when I am printing the $line variable and it is giving the values in the same line as follows. line : 1DWK 2RFK 4ERH. So it will try to match this value in the FILEB and it wont get matched. Because all the Ids are delimited by a new line in FILEB. So you need to use the different delimiter as space character and you need to use the split.