Sorry, forgot to mention that the command line option to output PDF 
directly seems not working if biblatex, and is suggested by the 
documentation:

--biblatex

Use biblatex for citations in LaTeX output. This option is not for use with 
the pandoc-citeproc filter or with PDF output. It is intended for use in 
producing a LaTeX file that can be processed with bibtex or biber.

I have written a bash script to chain everything together (pandoc to tex 
first and then use latexmk), but is curious why pandoc cannot do that.
​

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