Modifications to the original script allowed the usage of MITObim inside an HPC environment. Modifications include a new argument, --lfspath, to indicate the full path to the working directory in the local file system (same as -DIR:temp=<string> in mira manifest.conf).
MITObim_modified.pl is available at http://www.ib.usp.br/grant/anfibios/researchHPC.html.