I did an strace -f on the command, and here's the end of the output (path edited out):

[pid 24623] stat("/path/65.db.psq", {st_mode=S_IFREG|0666, st_size=811
+5, ...}) = 0
[pid 24623] open("/path/65.db.psq", O_RDONLY) = 6
[pid 24623] mmap(NULL, 8115, PROT_READ, MAP_PRIVATE, 6, 0) = 0x7f78165
+73000
[pid 24623] write(1, "AT5G51490.1.CDS\tAT4G00190.1\t46.0"..., 1340) = 
+1340
[pid 24623] write(1, "AT2G26450.1.CDS\tAT1G53830.1\t40.5"..., 1615) = 
+1615
[pid 24623] write(1, "AT1G11580.1.CDS\tAT3G14310.1\t50.1"..., 1286) = 
+1286
[pid 24623] write(1, "AT2G45220.1.CDS\tAT4G00190.1\t52.6"..., 1279) = 
+1279
[pid 24623] write(1, "AT3G14310.1.CDS\tAT3G14310.1\t100."..., 1270) = 
+1270
[pid 24623] write(1, "AT5G55590.1.CDS\tAT5G55590.1\t100."..., 1452 <un
+finished ...>
[download]

I guess this isn't a perl question, but it doesn't make sense to me that writing to a file would freeze.

It freezes because file descriptor 1 (stdout) is attached to a pipe and nobody is reading from the other side.

Why are you using open3 to launch the process?

Oh, I hadn't thought of that, my slightly extended code was:

    $pid=open3($wtr, '>&reader', $err, $cmd);
    waitpid($pid, 0);

    my %Results=();
    while(<$rdr>){
        chomp;
        @temp=split(/\t/);
        if(!exists($Results{$temp[0]}) || $Results{$temp[0]}<$temp[10]
+){
            $Results{$temp[0]}=$temp[10];
        }
    }
[download]

So I take it that I should've used waitpid after I finished "reading" the pipe. Duh(!) Moving waitpid til after <$rdr> worked. Upon reflection, I realized that the output from running this particular file was far larger than any other, and was thus the first to fill the I/O buffer.

In related news, I gave myself a crash course in buffering and also tried using IPC::Run() with pty, and worked too, but which is recommended?