Listen to everything the other monks have previously told you as far as asking a question on here. It is not totally clear what the goal of your script is, either. You simply want to read a fasta file and calculate the percentage of occurances for each nucleotide? I have done this before, so I will try to help you.
Also, It appears that you are trying to read a fasta file. Why are you shifting the file in the beginning? Please, do file handle like this instead:

my $file = '/path/to/file.txt';
open (my $fh, '<', $file) or die "Could not open file '$file' $!";
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Update: So, if you delete the subroutine reference  &process_nuc from your first while loop, the code sucessfully reads a fasta file into  $seq1
After that, you're gonna need to loop through it and increment each time a nucleo tide is found, then do your division for percentage.