LaTeX Beginner's Guide ⇒ BibTeX isn't working; my \cite are showing up as question marks (?)

[MABDALSALAM90]

I use the peer-reviewed J computer latex format, which used chicago-authordate bibliography style and am facing the following issues:

BibTeX isn't working well; my \cite are showing up as question marks (?) Even though I am certain that its in my bib file. Moreover, when the number of references in the main.tex file is less than 100, everything works normally, when I increase the number of references in my latex main.tex, the \bibliography style changed to a number and some of the references did not appear. 

[kaiserkarl13]

Please post a minimal working example