This message means that the system cut off the pulse before it was completed (usually this is because the conductivity of the solution is at the low end of the normal range). The pulse was applied; it is just going to be a little weaker than expected. So it is worthwhile to analyze the sample, keeping in mind that the transfection efficiency might be a bit lower. We don't recommend applying the pulse to the same cuvette again, as this will most likely result in high mortality of your cells.