Completely unrelated to your problem...

If you are interested in something more WYSIWYG than your $usage, you could try using a HERE DOC to eliminate all the quoting and newlines:

my $usage = <<EOF

usage: $0 [-flags] <fasta file> <output file> (must be all 1 type.
    ie all fasta NT, all fastq, all fasta fna)

etc...

EOF
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Or better yet, use POD and the Pod::Usage core module.

if( ( $#ARGV + 1 ) < 1 ) {
    die $usage;
}
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Another way to code this is:

die $usage unless @ARGV;
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