No citations/bibliography processed/produced when using \include

I use TextMate 2 to write my LaTeX documents. I've noticed that when I use \include to add chapters, my citations don't process, whereas when I use \input, they do. I would like my document to have page breaks at the chapters, thus I prefer to use \include. (The \includeonly command is also a very nice benefit.)

I compiled my document (cmd R) and noticed no .bbl was created. This is despite the fact that TextMate (with latexmk automatically runs LaTex and Biblatex multiple times for each compiling). I ran Biblatex independently. A .bbl for the main document was created, but was apparently empty, as when I compiled the document again the citations in the document did not appear, and there was no bibliography. I changed one of the chapters to \input and compiled, and the citations were processed and a bibliography (for those citations in that chapter only) was produced.

Am I doing something wrong? Why doesn't bibliographic material get produced with \include?

If I can't create a bibliography using \include, what is the easiest way to create page breaks for chapters using \input? I assume it would be to put \pagebreak before each \input command.

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In the normal documentclasses a \chapter always starts on a new page anyway, so you don't have to add anything. –  Torbjørn T. Aug 13 '13 at 16:28
maybe this can help: tex.stackexchange.com/questions/246/… –  Jonathan Aug 28 '13 at 19:19

The following exmaple shows, that biblatex in conjunction with biber has no limitations in that matter and can handle included files as well. The important thing to remember is: Run biber not bibtex on the basename.bcf which contains the information on what to cite of all included files.

\documentclass{report}
\usepackage{blindtext}
\usepackage{biblatex}
%a helper file
\begin{filecontents}{\jobname-Duck.tex}
\chapter{this is some duck chapter}
\cite{companion}
and \blindtext
\end{filecontents}
%another helper file
\begin{filecontents}{\jobname-Peng.tex}
\chapter{this is some penguin chapter}
\cite{aristotle:physics}
and \blindtext
\end{filecontents}
\begin{document}
test\cite{westfahl:space}
\include{\jobname-Peng}
\include{\jobname-Duck}

\printbibliography

\end{document}

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