I used the following in the end, using tee.exe - thanks for your tip!

$|++;
open (STDERR, ">&STDOUT");
#stuff
my $cmdout = `system command`;
print $cmdout;

[download]

And ran it using

perl code.pl |tee outfile.txt

In reply to Re^2: Capturing all (and I mean all) output to a file by flippy
in thread Capturing all (and I mean all) output to a file by flippy

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