It seems that bsub somehow finds out that its standard error is not connected to a terminal, and then refuses to print the message.
Can you check this theory by running bsub -k > some-file 2>&1 from the command line? If the error message shows up in some-file then that would be a work-around.

Another option is to check $? to see if bsub exited with a 0 status. Commands usually exit with a non-zero status when there is an error condition. This won't get you the output, but at least you can tell if there was a problem: 

my $output = qx("$command 2>&1");
if ($?) {
  # something wrong
}

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In reply to Re: How to trick this program (weird catch-the-output problem)? by pc88mxer
in thread How to trick this program (weird catch-the-output problem)? by rovf

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