Hello Duccio, The bug you are encountering has been fixed since the 2.1.1 release, and the fix will become part of the next Mauve software release. You can read about the bug here: http://sourceforge.net/tracker/index.php?func=detail&aid=1785300&group_id=181544&atid=897627
In the meantime, you can try to work around the bug by adding the --disable-cache option to the progressiveMauve command-line. Unfortunately the alignment will probably run even slower with this option, but it should finish. The command-line, which can be run from within the Mac Os X Terminal.app should look something like: /Applications/Mauve/Mauve.app/Contents/MacOS/progressiveMauve --output=/data/all_merged --backbone-output=/data/all_merged.backbone --output-guide-tree=/data/all_merged.guide_tree --disable-cache /data/genome1.fna [...] /data/genome20.fna Hope that helps, -Aaron Duccio Medini wrote: > Hi. > I'm re-posting with just header and footer of the console log: > > I'm trying to align 19 closely related genomes + 1 distantly related > with progressiveMauve 2.1.1 on a MacOSX 10.4 box. > It runs for about 14 hours, sending to the console meaningful logs, > than crashes with "error code 132". > It happens after a recursive anchor search, but several recursive > anchor searches had already been performed successfully. > The box is equipped with 2GB RAM, and the maximum Mauve RAM usage > appears to be 1.4GB, so it should not be a memory shortage problem. > What "error code 132" stands for? > > Any suggestions on how to fix it? > The complete console log follows. > > Thanks a lot in advance! > Duccio Medini > > > OS name is: Mac OS X arch: i386 > > Executing: > /Applications/Mauve/Mauve.app/Contents/MacOS/progressiveMauve > --seed-family --output=/data/all_merged > --backbone-output=/data/all_merged.backbone > --output-guide-tree=/data/all_merged.guide_tree --muscle-args=-maxmb 900 > > /data/genome1.fna > > [....] > > /data/genome20.fna > Sequence loaded successfully. > /data/genome1.fna 4751080 base pairs. > Sequence loaded successfully. > /data/genome2.fna 2153922 base pairs. > Sequence loaded successfully. > > [...] > > /data/genome20.fna 2184406 base pairs. > Using weight 15 mers for initial seeds > Creating sorted mer list > Create time was: 3 seconds. > > [....] > > Searching with seed pattern 11110011010101011001111 > Creating sorted mer list > Create time was: 3 seconds. > > [...] > > Creating sorted mer list > Create time was: 2 seconds. > 0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%.. > 11%..12%..13%..14%..15%..16%..17%..18%..19%..20%.. > 21%..22%..23%..24%..25%..26%..27%..28%..29%..30%.. > 31%..32%..33%..34%..35%..36%..37%..38%..39%..40%.. > 41%..42%..43%..44%..45%..46%..47%..48%..49%..50%.. > 51%..52%..53%..54%..55%..56%..57%..58%..59%..60%.. > 61%..62%..63%..64%..65%..66%..67%..68%..69%..70%.. > 71%..72%..73%..74%..75%..76%..77%..78%..79%..80%.. > 81%..82%..83%..84%..85%..86%..87%..88%..89%..90%.. > 91%..92%..93%..94%..95%..96%..97%..98%..99%.. > Searching with seed pattern 11110110010101001101111 > > [.........] Footer: > > Previous anchoring score: 1.39838e+08, new anchor score: 1.39496e+08 > propagating ancestral breakpoints > performing a gapped alignment > 0%..1%..2%..3%..4%..5%..6%..7%..9%.. > 10%..12%..13%..14%..15%..16%..17%..18%..19%.. > 20%..22%..23%..25%..26%..27%..28%.. > 30%..31%..32%..33%..34%..35%..36%..37%..38%..39%.. > 40%..41%..42%..43%..44%..45%..47%..48%..49%.. > 50%..52%..53%..54%..55%..56%..57%..59%.. > 60%..62%..63%..64%..65%..66%..67%..69%.. > 70%..72%..73%..74%..76%..77%..78%..79%.. > 80%..81%..82%..83%..84%..87%..88%..89%.. > 91%..92%..93%..95%..97%.. > 100%..Fix left ends > done. > Aligning node 25 to 28 via 24! > get ancestral matches > Performing Sum-of-pairs Greedy Breakpoint Elimination > construct LCB tracking matches > There are 12897 tracking matches > There are 51084 / 502983 components used > init tracking match LCB tracking > pairwise score tracking matches > get pairwise LCBs > there are 2761 pairwise LCBs > scaling bp penalty by conservation weight: > 0.142939 > 0.168289 > > scaling bp penalty by bp weight: > 0.176786 > 0.3375 > Greedy BPE > Scoring with scaled breakpoint penalty: 54237.2 > 1%..2%..3%..4%..5%..6%..7%..8%..9%.. > 10%..11%..12%..13%..14%..15%..16%..17%..18%..19%.. > 20%..21%..22%..23%..24%..25%..26%..27%..28%..done > Arrived at 22 intervals > Adding unaligned intervals > addUnalignedIntervals yields 62 intervals > Merging unaligned intervals > Marbling gaps > Propagating descendant breakpoints > descendant 0(25) has 16 intervals > descendant 1(28) has 1 intervals > propagateDescendantBreakpoints yields 37 intervals > Creating ancestral ordering > Previous anchoring score: - 1.79769e+308, new anchor score: 2.38672e+08 > Backing up alignment tree... > propagating ancestral breakpoints > recursive anchor search > Exited with error code: 132 > > ---- End of console log ---- > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > ------------------------------------------------------------------------ > > _______________________________________________ > Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users > ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
