Hi,
Our group compiled MAUVE on Red Hat Linux using instructions provided on
MAUVE's web page. We wanted to reproduce the results for 5 Salmonella genomes
from ERIC's web page. We used both mauveAligner and progressiveMauve with the
default options, but could not obtain the results from the web page. Moreover,
progressiveMauve crashed for the default setup with the following error message:
cga doesn't fit
cga.RightEnd(cga_seq) 292746
RightEnd(my_seq): 5133713
cga.LeftEnd(cga_seq) 292724
LeftEnd(my_seq): 4836644
cga.AlignmentLength(): 23
AlignmentLength(): 292727
cga doesn't fit
cga.RightEnd(cga_seq) 293601
RightEnd(my_seq): 5133713
cga.LeftEnd(cga_seq) 293579
LeftEnd(my_seq): 4836644
cga.AlignmentLength(): 23
AlignmentLength(): 292727
progressiveMauve:
/local/software/mauve/include/boost-1_34_1/boost/dynamic_bitset/dynamic_bitset.hpp:952:
Unknown( ) : Assertion `pos < m_num_bits' failed.
Aborted
We tried to change the breakpoint penalty as suggested in Example 7 of the
User's manual and we were able to get some results. However, results were
frequently irreproducible: in some runs the program crashed for the given
value of the weight parameter, with an error message similar to the previous
one, while in other runs with identical input the program worked fine. Has
anyone had similar experience and what could be the reason for such behavior?
In general, we are not sure how to select parameters for progressiveMauve when
the default setup does not work and would appreciate any advice in that matter.
Thank you very much,
Nela Zavaljevski
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