Hi Paulina, what version are you using? This looks like a bug that was in 2.4.0. Perhaps you could revert to v2.3.1 or use the latest snapshot: http://darlinglab.org/mauve/snapshots/2015/2015-02-25/MacOS/Mauve-snapshot_2015-02-25.dmg
I'm working to push a new release with these fixes ASAP but there are a few other issues that need resolution first. Best, -Aaron On Fri, 2015-03-20 at 14:04 +0000, Paulina Dmitrievna Pavinski Bitar wrote: > Good morning, > Wondering if anyone has a suggestion for me. > I used progressivemauve to align 48 genomes and got a gibberish > alignment because, silly me, I did not order my contigs first. > So re-ordered the contigs using Mauve Contig Mover (one at a time, > using the same reference) and then tried to realign the 48 genomes > with progressivemauve. > No luck. > After two hours progressivemauve exited with this error: > > > > > Greedy BPE > Scoring with scaled breakpoint penalty: 150573 > 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%..done > Arrived at 5 intervals > Adding unaligned intervals > addUnalignedIntervals yields 15 intervals > Merging unaligned intervals > Marbling gaps > Propagating descendant breakpoints > descendant 0(61) has 3 intervals > descendant 1(64) has 1 intervals > propagateDescendantBreakpoints yields 7 intervals > Creating ancestral ordering > Previous anchoring score: -1.79769e+308, new anchor score: 2.31866e+08 > Backing up alignment tree... > propagating ancestral breakpoints > recursive anchor search > 0,0 have 62 new matches outside LCBs > 1,0 have 77 new matches outside LCBs > Caught signal 11 > Cleaning up and exiting! > Temporary files deleted. > > > > > > > Then I tried it again, no changes, just to see if maybe > progressivemauve had simply crashed as it sometimes does for me for no > apparent reason and got this error after two hours: > > > Greedy BPE > Scoring with scaled breakpoint penalty: 150573 > 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%..done > Arrived at 5 intervals > Adding unaligned intervals > addUnalignedIntervals yields 15 intervals > Merging unaligned intervals > Marbling gaps > Propagating descendant breakpoints > descendant 0(61) has 3 intervals > descendant 1(64) has 1 intervals > propagateDescendantBreakpoints yields 7 intervals > Creating ancestral ordering > Previous anchoring score: -1.79769e+308, new anchor score: 2.31866e+08 > Backing up alignment tree... > propagating ancestral breakpoints > recursive anchor search > libc++abi.dylib: terminating > 0,0 have 62 new matches outside LCBs > 1,0 have 77 new matches outside LCBs > > > Very similar but a little different. > I’m using the MCM output files totally unchanged. The data is the same > but now in theory better suited for alignment since it’s been > reordered. Other such errors people have mentioned are due to the > format of the files. Could that be a problem and so late into the > program – 2 hours? What else could it be? Would really love to see > this work. > > > Thank you, > Paulina > > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
