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
