Quick note. When I was comparing the protein sequences from C. glomerans PW2 to those in E. coli K12 MG1655, the program would get stuck with this sequence:
>gi|328954742|ref|YP_004372075.1| MSKTIPELTLDNFDLVMQSKLPVLVDFWAPWCGPCRTLSPIVEQVAEEMSERITVAKCNVDENQDLAMKYGVMS IPTLVLFRDGAEVSRTVGAMPKPKLVAEIEKNL
I could not figure out the problem, but found that compiling with gcc-4 installed by fink fixed the problem. I just had to change this line in the “Makefile.os_x86_64” file:
CC= cc -O -g -arch x86_64 -msse2
CC= /sw/bin/gcc-4 -O -g -arch x86_64 -msse2
I am starting to suspect that the gcc that comes with Xcode is faulty.