This line:

if ( <INPUT_FILE> =~ m/[^actgACTG]/ ) {
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calls <> (i.e., readline) only once (in scalar context), therefore only the first line of the file is read in and tested. To test the whole file, you need a loop. For example (untested):

my $ok = 1;

while (<INPUT_FILE>)
{
    chomp;

    if (/[^actg]/i)
    {
        print "File contains something besides actg sequence.\n";
        $ok = 0;
        last;
    }
}

print "good!\n" if $ok;
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And yes, the chomp is necessary, otherwise each line (except perhaps the last) will contain a newline character and so fail the regex test.

Hope that helps,