Hello Sarah, The troublesome behavior mauveAligner exhibits on your problem dataset is that it repeatedly attempts to extend LCB boundaries until it exhausts all available memory. Although LCB boundaries are being improved with each iteration, the gain is usually small and probably doesn't justify the long runtime and excessive memory usage.
An upcoming Mauve release will limit the number of attempts at LCB extension to avoid the infinite vortex of LCB extension that you and others periodically experience. I am hopeful that a new release can be ready in the next month or so. In the meantime, a workaround is to uncheck the "LCB Extension" option, which is available in the alignment parameters tab of the Mauve GUI. The option needs to be unchecked, even if it's grayed out (disabled). If it's grayed out but still checked, then temporarily enable "Full Alignment" to uncheck "LCB Extension". Hope that helps... -Aaron > Hello, > I am getting an error very similar to the one that Lance Palmer had in > April. The mauve console log is attached. From the advice to him, I > see that > 'the error message could indicate either a formatting problem in the > sequence > input files, a shortage of memory on your windows machine, or a bug in > Mauve.' > The sequence input files align without error with other sequences, only > this particular combination produces an error. Thus, I think the input > files are appropriately formatted. > I would greatly appreciate any help in getting this alignment running > without error. > thank you, > Sarah Cousins > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/_______________________________________________ > Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
