Your input database should consist of a file containing sequences in fasta format. In the example below, the file is 'mini-drosoph.s'.
Maxsize parameter: The maximum dataset size in characters. Determine the number of characters in your dataset by typing 'wc -c filename'. e.g.
For this dataset, the maxsize parameter has to be set to greater than 506,016, so we will use 600000.Set up a batch script along the lines of the ones below:
Batch script for Meme 4.6.1
// The above tips are from http://biowulf.nih.gov/apps/meme.html
btw, the above script use PBS (Portable Batch System) submission system. Alternatively, there are other options, like LoadLeveler (Champion), LSF (Lonestar). There are syntax comparison here. Also, more detail for SGE and PBS here.