The problem here is that you are using readline() on a binary file.

You are relying on the fact that many binary files happen to contain bytes that look like line ends.

And using for with a file handle means you are slurping the whole file into a list.

And if the file contains (say) a lot of packed binary integers, it could mean that you are reading and writing the file in a gazillion iddy-biddy chunks.

You say you've tried sysread and syswrite but don't show any code, or how the results failed -- ie. did you compare the input and output files?

Your best bet would be to replace the read/write loop above with something like:

open OUT ...
{
    local $\;
    my $buffer;
    while( read( STDIN, $buffer, 4096 ) ) {
        print OUT $buffer;
    }
}
close OUT;
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