Comment # 1 on bug 992058 from Dr. Werner Fink

Hmmm ... the so called pool files are part of the executable, e.g.

  ls -l /usr/bin/pdflatex
  lrwxrwxrwx 1 root root 6 Dec  1  2015 /usr/bin/pdflatex -> pdftex

that is the pool `file' is included in /usr/bin/pdftex  ... then only question
is how you get a format file with this binary?  Do you have mixed
installations, that is do you have e.g. an other TeXLive or TeX installation
around?

I ask this because normally there is only on binary around and this is used to
create the format file.  In other words: on a cleam installation this error can
not happen.

You might run as root

  fmtutil-sys --refresh 1>&2 | tee fmtutil.log

and attach the resulting file fmtutil.log.  Does it work after this command?