Clarification on running pindel on individual samples

[ashokrags]

hi,
I wanted to get some clarification on running pindel. Is it the case that I should only run Pinlde with multiple samples and not run each sample individually? When i run each sample individually, the only output generated is for the _DD file, all other files are empty. However, when I run multiple samples, 5 samples in my case, it generates all outputs.
Am I missing something simple in this case or is this the default behavior for pindel. I am using Pindel version 0.2.5b9, 20160729.
Much obliged for any quick clarification in this regard.
Cheers
Ashok