Hi Cristina, not a bother, no need to apologize! In fact, this is really useful information. I downloaded those two genomes from the NCBI genbank ftp site and tried to reproduce the error on Mac or Linux. I ran the alignment 10 times and on Mac it did crash on one of those 10 runs at the same place you experienced the crash, and on Linux it reported errors (but did not crash) on some but not all of the runs. So it seems there is an elusive data-dependent and nondeterministic bug being triggered here. I will need to dig deeper to understand what's gone wrong, but in the meantime you might find that running the same alignment again will work.
Best, -Aaron On Thu, 2015-01-29 at 11:27 +0900, cav00004 wrote: > Dear Aaron, > > Sorry for constantly bothering you. > I've been running alignment of complete bacterial genomes that I have > downloaded from ncbi. Not a big work, only 5 genomes ob about 4Mb maximum. > After successfully aligned the 5 of them and a subset of 3... I wanted to > align only 2 of them and an error occurred at the beginning of the task. > I copy here the whole console text: > > Running alignment. > Executing > /Applications/Mauve 2.4.0/Mauve.app/Contents/MacOS/progressiveMauve > --output=/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome > Comparison/DDBJ_WGS/MAUVE alignemnts/Complete Apast (2s) > --output-guide-tree=/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome > Comparison/DDBJ_WGS/MAUVE alignemnts/Complete Apast (2s).guide_tree > --backbone-output=/Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome > Comparison/DDBJ_WGS/MAUVE alignemnts/Complete Apast (2s).backbone > /Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome Comparison/DDBJ_WGS/MAUVE > Input sequences/Acetobacter pasteurianus IFO 3283-01.gb > /Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome Comparison/DDBJ_WGS/MAUVE > Input sequences/Acetobacter pasteurianus 386B.gb > Storing raw sequence at > /var/folders/sr/w5fjtzj91t72f0kjm0s3ny9m0000gn/T/rawseq7102.000 > Sequence loaded successfully. > /Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome Comparison/DDBJ_WGS/MAUVE > Input sequences/Acetobacter pasteurianus IFO 3283-01.gb 2907495 base pairs. > Storing raw sequence at > /var/folders/sr/w5fjtzj91t72f0kjm0s3ny9m0000gn/T/rawseq7102.001 > Sequence loaded successfully. > /Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome Comparison/DDBJ_WGS/MAUVE > Input sequences/Acetobacter pasteurianus 386B.gb 2818679 base pairs. > Using weight 15 mers for initial seeds > Creating sorted mer list > Create time was: 1 seconds. > Creating sorted mer list > Create time was: 1 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%..done. > using default bp penalty: 150144 > using default bp estimate min score: 450432 > Starting with 2928 multi-matches > Computing genome content distance matrix... > > > Genome conservation distance matrix: > 0 0.0942431 > 0.0942431 0 > > Writing guide tree to /Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/Genome > Comparison/DDBJ_WGS/MAUVE alignemnts/Complete Apast (2s).guide_tree > reading tree... > initializing alignment tree... > Constructing seed occurrence lists for repeat detection > Calculating pairwise breakpoint distances > Pair 0, 1 has 759 initial LCBs > Using scaled bp penalty: 303163 > Pair (0,1) has 2 well-supported breakpoints > genome content distance matrix: > 0 0.0942431 > 0.0942431 0 > > bp distance matrix: > 0.9 0.0428571 > 0.0428571 0.9 > > Aligning... > Aligning node 1 to 2 via 0! > get ancestral matches > Performing Sum-of-pairs Greedy Breakpoint Elimination > construct LCB tracking matches > There are 2261 tracking matches > There are 4522 / 6783 components used > init tracking match LCB tracking > pairwise score tracking matches > get pairwise LCBs > there are 768 pairwise LCBs > scaling bp penalty by conservation weight: > 0.0942431 > > > scaling bp penalty by bp weight: > 0.0428571 > > Greedy BPE > Scoring with scaled breakpoint penalty: 92578 > 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%..done > Arrived at 5 intervals > Adding unaligned intervals > addUnalignedIntervals yields 16 intervals > Merging unaligned intervals > Marbling gaps > Propagating descendant breakpoints > descendant 0(1) has 1 intervals > descendant 1(2) has 1 intervals > propagateDescendantBreakpoints yields 5 intervals > Creating ancestral ordering > Previous anchoring score: -1.79769e+308, new anchor score: 1.27763e+08 > Backing up alignment tree... > propagating ancestral breakpoints > recursive anchor search > 0,0 have 151 new matches outside LCBslibc++abi.dylib: terminating > > Exited with error code: 134 > > > Thank you for your help!! > > Cristina > > ------------------------ > Cristina Andres-Barrao, PhD. > cav00...@nodai.ac.jp > Laboratory of Fermentation Biochemistry > Department of Fermentation Sciences > Faculty of Applied Biosciences > Tokyo University of Agriculture > 1-1-1 Sakuragaoka, Setagaya-ku > Tokyo 156-8502, Japan > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. 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