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open SAVEERR, ">&STDERR";
open SAVEOUT, ">&STDOUT";
...
open STDERR, ">&main::SAVEERR";
close STDOUT;
open STDOUT, ">&main::SAVEOUT";

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String[] cmd ={"/home/seaver/MONSTER/monster", "-i" + jobID, filePath 
++ pdbFileName};
        try{
...
        }catch (Throwable t){
            t.printStackTrace();
        }