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I am using Texworks Version 0.6.2 (MiKTeX 2.9.6350 64-bit). Originally I had a bibliography but I have taken it out and the error is the same.

I am running a file containing:

\documentclass{article}

\begin{document}
Test
\end{document}

pdfLaTeX gives:

This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6350 64-bit) entering extended mode (WorkedExample.txt LaTeX2e <2017-04-15> Babel <3.10> and hyphenation patterns for 75 language(s) loaded. ("C:\Program Files\MiKTeX 2.9\tex\latex\base\article.cls" Document Class: article 2014/09/29 v1.4h Standard LaTeX document class ("C:\Program Files\MiKTeX 2.9\tex\latex\base\size10.clo")) (WorkedExample.aux) [1{C:/ProgramData/MiKTeX/2.9/pdftex/config/pdftex.map}] (WorkedExample.aux) )<C :/Program Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr10.pfb> Output written on WorkedExample.pdf (1 page, 11236 bytes). SyncTeX written on WorkedExample.synctex.gz. Transcript written on WorkedExample.log.

pdfLaTeX+MakeIndex+BibTeX gives error:

This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6350 64-bit) entering extended mode (C:/Bugs/WorkedExample.txt ! Undefined control sequence. l.1 \documentclass {article} ?

MakeIndex (alone) gives:

Couldn't find input index file WorkedExample nor WorkedExample.idx. Usage: makeindex [-ilqrcgLT] [-s sty] [-o ind] [-t log] [-p num] [idx0 idx1 ...]

BibTeX gives:

This is BibTeX, Version 0.99d (MiKTeX 2.9.6350 64-bit) The top-level auxiliary file: WorkedExample.aux I found no \citation commands---while reading file WorkedExample.aux I found no \bibdata command---while reading file WorkedExample.aux I found no \bibstyle command---while reading file WorkedExample.aux (There were 3 error messages)

But worked fine when I had a citation present so I don't think this is the problem.

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    The last two are just warnings as they have no data to work on. The pdfLaTeX+MakeIndex+BibTeX gives error: seems to indicate that it is configured incorrectly, it seems it is running pdftex not pdflatex. – daleif Jan 8 at 13:54
  • Yes I noticed that but both pdfLaTeX and pdfLaTeX+MakeIndex+BibTeX are using pdftex so why does one work and not the other? If that is the problem how do I change them to run pdflatex? I have looked at Tool Configuration and pdfLaTeX is using the program miktex-pdftex.exe and pdfLaTeX+MakeIndex+BibTeX is using texify.exe. Thanks.@daleif – Green Fish Jan 8 at 14:07
  • pdflatex is a special call to pdftex with a given format. Since the the latter example you give gives error on \documentclass it is a clear indication that the latex format is not being used in that call. – daleif Jan 8 at 14:31
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The document was saved as WorkedExample.txt, when saved as WorkedExample.tex or WorkedExample.ltx it compiles fine.

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