وَقَى يَقِي is separated doubly weak: wāw in the first root position and yāʾ in the third, with qāf between them.
StageFormWhat happened
PerfectوَقَىRoot و ق ي
ImperfectيَقِيLoss of initial wāw
Jussiveلَمْ يَقِLoss of final weak letter
CommandقِImperative from the shortened stem
One written consonant in the command does not mean the original root contains one consonant.