From Genome Analysis Wiki
If you are using version 0.4.4 and under, please go to our wiki page to download the newest version [[RAREMETAL]]. There was a bug in makefile in older versions of RAREMETAL that could cause this error and it has been fixed. For a quick fix, please go to /raremetal/src and open "Makefile". Then comment out the lines at the bottom of raremetal/src/Makefile that set LD_LIBRARY_PATH. Try compiling and see if it works.