Not sure if this has been addressed, but thought I'd let folks know how I
dealt with this...
The error message is the result of a sanity check in an older version of
libMems/Interval.h (visible here:
http://gel.ahabs.wisc.edu/apidocs/libMems/Interval_8h-source.html) which
is present in the Mauve binary distribution - looks like it's checking for
sequences greater than a Giga-base, and bailing. The current version of
the file in the source code snapshot has removed the sanity check, so if
you rebuild Mauve from the current source snapshot, it works for larger
sequences. I also used an older version of the boost distribution to get
mauve to build successfully (boost_1_40_0). I was occasionally seeing
memory faults, but when I increased my stacksize (via ulimit -s) to
something huge (10 GB) it seemed to solve the problem. Just successfully
aligned human and chicken genomes (took 2 days on a machine with 70 GB ram).
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