I'm not an expert on IPC3::Open , but here is a trick from the docs which combines STDERR to STDOUT by setting STDOUT to false.

#!/usr/bin/perl
use warnings;
use strict;
use IPC::Open3;

#interface to "bc" calculator 
#my $pid = open3(\*WRITE, \*READ, \*ERROR,"bc"); 
my $pid = open3(\*WRITE, \*READ,0,"bc");
            #if \*ERROR is false, STDERR is sent to STDOUT  
while(1){
print "Enter expression for bc, i.e. 2 + 2\n";
chomp(my $query = <STDIN>);

#send query to bc 
print WRITE "$query\n";

#get the answer from bc 
chomp(my $answer = <READ>);

print "$query = $answer\n";
}
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