I can't test at the moment, but I wrote on the topic of running external commands here, including the advice to check $? for errors and that interpolating variables into the shell is problematic - what does @SetBCs contain exactly? But I think much more important here is: just do this in plain Perl in the first place, a while(<>) loop is fairly easy to implement (perlintro). At the very least you can switch to a module like IPC::System::Simple.