i know it's a bit late and you probably solved the problem but here is an extra solution

if the output of the job is some kind of a file or a bunch of files that you cp in some directory you can check if all the files are there and then continue:

my $qsub = qx/qsub -pe mpi 5 -t 1:$filecount:2 $bash/;
print "$qsub\n";

# check for sge to finish 
my $r;
my $fileoutcount = $filecount + 2;

while($r < $fileoutcount){
    
    opendir(DIR, "./out/BLAST/out") || die "$!";
    $r = 0;
    foreach (readdir DIR){
        $r++;
    }
    closedir DIR;
    sleep 500;
}
[download]

this was my solution, running the job on sge by bash script. and now i'm looking for a more direct approach, and SGE module looks pretty ok for now.

baxy