I recently upgraded from Ubuntu 12.04 to Ubuntu 13.10 and had to reinstall TexLive 2013 and TeXWorks. Ordinary typesetting with pdfLaTeX works fine. However, when I try to run BibTeX, the only console output is "Permission denied" and it doesn't compile the bibliography.
I have tried compiling on another machine with the same tex and bib files and it works fine, so I know my source files are fine and the problem must be with how LaTeX is installed.
I thought since the error mentioned permissions, that somehow I had installed it so that only the root user can access BibTex. I tried opening TeXWorks as root (via sudo texworks) and then used that version of TeXWorks to compile, but it couldn't even compile using pdfLaTeX.
How can I change the settings of TeXWorks and/or TeXLive to make BibTeX compile again?