Batch mode inputs

Hi Pat,

Apologies if this has already been covered but I was unable to find a solution.

I have been trying to set up a batch file script so I can run my analysis on a cluster we have at our uni. However, I am unsure about how to get appropriate inputs for screen.seqs. After running summary.seqs on the alignment, I then get;

Start End NBases Ambigs Polymer
Minimum: 1044 1058 5 0 2
2.5%-tile: 1044 8419 332 0 4
25%-tile: 1044 10243 430 0 4
Median: 1053 10352 446 0 5
75%-tile: 1071 13125 449 0 5
97.5%-tile: 3655 13871 449 0 7
Maximum: 43107 43116 450 0 9

of Seqs: 24915

For this example I would like to screen at start=3655 (97.5%tile), end=8419(2.5%tile), so I am not sure how to input this in a batch mode. I had a look at the optimise and criteria but not sure how to apply that to my example.

Also with batch mode, does it automatically take the appropriate group and name files throughout the analysis?

and also what is the max number of processors that mothur can utilise?