Only problem I had was with not-hypothetical.pl. The script (actually fastacmd) did not like the string "Y.pestisbig-experiment" which was inserted into the first line of yp-unique. If you remove it manually then not-hypothetical.pl runs, but it does not write any output to yp-real. Possibly because it doesn t find any hypothetical entries in yp-unique (I could not find any from manual inspection).
