Hello Inaki, The error message indicates that progressiveMauve was unable to allocate additional memory, probably meaning that it needs more RAM to compute alignments on your particular dataset.
If you are using progressiveMauve 2.1.x, I would strongly recommend removing the --seed-family option to reduce memory consumption. It may be possible to also set --scoring-scheme=ancestral and get an alignment using less memory, but the behavior of the ancestral scoring scheme has not been tested on a broad range of datasets, it may crash, and alignments produced should be inspected for quality. hope that helps, -Aaron [EMAIL PROTECTED] wrote: > When I try to align 16 Mycobacterium genome sequences using > progressiveMauve I always get this error message at the end of the > execution: > Aligning node 23 to 24 via 22! > get ancestral matches > Performing Sum-of-pairs Greedy Breakpoint Elimination > construct LCB tracking matches > There are 208846 tracking matches > There are 835175 / 6891918 components used > init tracking match LCB tracking > pairwise score tracking matches > get pairwise LCBs > there are 11483 pairwise LCBs > scaling bp penalty by conservation weight: > 0.0808374 0.0761207 > > > scaling bp penalty by bp weight: > 0.00189274 0.0113565 > > Greedy BPE > Scoring with scaled breakpoint penalty: 110956 > 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%..done > Arrived at 2 intervals > Adding unaligned intervals > addUnalignedIntervals yields 5 intervals > Merging unaligned intervals > Marbling gaps > Propagating descendant breakpoints > descendant 0(23) has 1 intervals > descendant 1(24) has 2 intervals > propagateDescendantBreakpoints yields 3 intervals > Creating ancestral ordering > Previous anchoring score: -1.79769e+308, new anchor score: 3.65577e+08 > Backing up alignment tree... > propagating ancestral breakpoints > recursive anchor search > terminate called after throwing an instance of 'std::bad_alloc' > what(): std::bad_alloc > Aborted > > this is the comand I enter (Red Hat Enterprise Linux 5 ): > > progressiveMauve --output=mycobacterium_alignment.xmfa > --backbone-output=mycobacterium_backbone NC_000962.gbk NC_002755.gbk > NC_002945.gbk NC_008595.gbk NC_008611.gbk NC_008726.gbk > NC_009077.gbk NC_009525.gbk NC_010397.gbk NC_002677.gbk NC_002944.gbk > NC_008146.gbk NC_008596.gbk NC_008705.gbk NC_008769.gbk > NC_009338.gbk NC_009565.gbk > > Any idea about the problem? > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users > ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
