While praying sunnah prayer in mosque iqamah is 
called
Question

                What should one do if one is praying the sunnah prayer 
in the mosque and the iqamah is called?
Praise be to Allah.If a person enters the mosque and is praying the sunnah while the 
iqamah is called, then the best opinion in this case is that if he is in 
his second rak‘ah, he should shorten it, and if he is in the first 
rak‘ah, he should just break his prayer and enter the congregation 
with the Imam1. The evidence for this comes from what Imam 
Muslim has narrated in his Sahih:
Prophet 
 (peace be upon him) said: If iqamah is 
called for the prayer then there is no prayer except the 
obligatory one. 
  (Sahih Muslim, 1/493) 
So, if one has performed the ruku‘ for the second rak‘ah, then he 
should complete the prayer, and if not, then he should discontinue 
because what is left from his sujud and tashahhud is not needed any 
more. Moreover, he should break without salaam, and it is enough 
to have the intention in the heart, contrary to common 
misconception.