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I am preparing to submit to a journal using a template downloaded from the "LaTeX" hyperlink at (https://academic.oup.com/bioinformatics/pages/submission_online). This downloads a .zip file called cabios.template.zip.

This .zip file contains .sty files, main.tex file, and main.bib file. It also contains a Sample.pdf file. I am unsure how to convert the main.tex file to look like the Sample.pdf file. So, far, I tried this approach:

pdflatex main
bibtex main
pdflatex main
pdflatex main

The bibtex command resulted in two Errors:

I found no \bibdata command---while reading file main.aux
I found no \bibstyle command---while reading file main.aux

It seems the main.bbl file is empty. On another part of their site, they state: "If you use bibtex, please use the bibliography style named natbib.bst". So, I also tried:

pdflatex main
bibtex natbib
pdflatex main
pdflatex main

And received a message:

I couldn't open file name `natbib.aux'

When I try the code above, I am able to generate a file main.pdf. However, it looks different than Sample.pdf, especially with text and corner lines in the margins. I am trying to make sure I use the correct conversion of main.tex to main.pdf, so that I am following the expected format correctly.

Any advice is greatly appreciated (and sorry if this is a newbie question).

  • 1
    If you use latexmk -pdf main.tex, it will automate this for you, provided that the commands in main.tex incorporate the bibliography appropriately. – pentavalentcarbon Feb 5 '18 at 17:27
  • Welcome to TeX.SX! There is no natbib.bst that I know of. You should do bibtex main, anyhow; an empty .bbl file may mean no \cite command in your document. – egreg Feb 5 '18 at 17:59
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Your first approach is correct:

pdflatex main
bibtex main
pdflatex main
pdflatex main

And @pentavalentcarbon's suggestion works too:

latexmk -pdf main.tex

The error:

I found no \bibdata command---while reading file main.aux

I found no \bibstyle command---while reading file main.aux

means that there is no \cite command (or similar, like \citet or \citep) in the document. This means that there is no need to run bibtex.

The .bbl file is empty, as you noted, because there is no \cite in the main document.

Once you start to write your manuscript the error will disappear and the .bbl file will be written as needed.

As for the difference between the sample.pdf and the main.pdf, it's not your fault. The sample.pdf was produced with a different source file, so it will not be exactly equal.

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