use Data::Dumper;
use IO::Handle
STDOUT->autoflush;

...upload file, etc...

alignSequences("$upload_dir/$filename","$upload_dir/$filename.out");

sub alignSequences {
    my $filename = shift;
    my $fileout = shift;
    open(MSA,"/usr/local/bin/mafft --auto 2>&1 $filename 1> $fileout |") or die "MSA failed: $!\n";  # Redirect STDOUT to a file and STDERR to STDOUT
    while ( <MSA> )
    {   
        print OUTFILE Dumper($_);  # When I print to Dumper, everything with a \r is part of the same $VAR print statement
    }   
    close MSA;
}