What is the reason for signals ceasing in the middle of a pyrosequencing run?

The cartridge needle can be blocked or damaged, causing a dispensation error. Clean the cartridge following the guidelines or repeat the run with a new cartridge. On the other hand, if high amounts of template have been used resulting in very high signals (>100 RLU), the substrate for the sequencing reaction might be depleted. In this case, template conditions should be optimized.