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my cluster limits the number of jobs I can submit, using array jobs gets around this requirement and maybe it will help other people who face the same problem. These changes also consolidate all the error messages so there aren't many many files produced by the cluster. The previous version of --use-cluster is still supported, I've added an "--SGEarray" option to be used in conjunction with "--use-cluster". Array job names can be designated with the "--job-name" option for queue control purposes.