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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

to

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.

See ya!

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