Check your file with

perl -mcharnames -e '<> =~ m/([^atcg])/i; print charnames::viacode(ord
+ $1), "\n"' ATCG_FILE
[download]

I created one file in Vim, typed 'atcgATCG' there, saved it, run the one-liner and got:

LINE FEED
[download]

Many editors add newline to the end of a file when they save it.