Yikes, I must've broken a mirror or crossed a black cat recently :-/ That seems to be yet another bug and one that may not be trivially fixable. May I suggest that you try version 2.0.0? It seems that in the process of tuning alignment parameters in 2.1.x for high positive predictive value, sensitivity was accidentally compromised in alignments with larger numbers of taxa. Until a 2.2.0 release, it may be better to stick with 2.0.0 for datasets like yours. One of the outstanding problems with 2.0.0 on linux was a crash during recursive anchor search; the same issue which --disable-cache addresses in 2.1.0, and I have created a special 2.0.0 build for linux-x64 with this issue fixed: http://gel.ahabs.wisc.edu/mauve/downloads/misc/progressiveMauve_2.0.0_linux_x64_ghostfix.tar.gz
If you move or copy progressiveMauve after untarring the archive, be sure to also copy muscle_aed into the same directory. I can't guarantee it will work, 2.0.0 is certainly not bug-free, but with luck it may get you an alignment sooner than I can make a 2.2.0 release. Hope that helps, -Aaron On Sat, 2008-02-23 at 20:16 -0800, Morgan Langille wrote: > Hi Aaron, > > Thanks for the fix, but it ended up crashing again at a different > location. It looks like it is looking for a library that is in your > directory. > > Do you think you could provide a fix? > > Here is the error: > > Greedy BPE > Scoring with scaled breakpoint penalty: 22036.4 > 1%..2%..3%..4%..5%..6%..7%..8%..9%.. > 10%..11%..done > Arrived at 115 intervals > Adding unaligned intervals > addUnalignedIntervals yields 344 intervals > Merging unaligned intervals > Marbling gaps > Propagating descendant breakpoints > descendant 0(1) has 481 intervals > descendant 1(10) has 241 intervals > propagateDescendantBreakpoints yields 835 intervals > Creating ancestral ordering > Previous anchoring score: 6.51848e+07, new anchor score: 6.45947e+07 > propagating ancestral breakpoints > performing a gapped alignment > > 0%.. > 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%.. > 82%..86%..87%..88%..89%.. > 90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..Fix left ends > > done. > performing iterative refinement > > 0%.. > 33%..34%..35%..36%..37%..38%..39%.. > 40%..41%..42%..43%..44%..45%..46%..47%..48%..49%.. > 50%..51%..52%..53%..54%..55%..cga doesn't fit > cga.RightEnd(cga_seq) 73994 > RightEnd(my_seq): 4223132 > cga.LeftEnd(cga_seq) 1 > LeftEnd(my_seq): 4149139 > cga.AlignmentLength(): 73994 > AlignmentLength(): 89033 > Unhandled gnException: Exception SeqIndexOutOfBounds thrown from > Unknown() > in > /home/a.darling/development/build_2.1.1/include/libMems-1.5/libMems/CompactGappedAlignment.h > 527 > > terminate called after throwing an instance of 'genome::gnException' > Aborted > > > Aaron Darling wrote: > > Hi Morgan, > > > > Indeed, you have discovered a problem specific to the 64-bit linux build > > of Progressive Mauve 2.1.1. It starts "waiting" and never stops. The > > root of the problem is that the Mauve release build and testing system > > has not yet been automated across all compute architectures (i.e. 32/64 > > bit, windows, linux, etc), and a bug slipped through in the 64-bit linux > > build. > > > > As near-term workaround I have built a replacement for the 64-bit linux > > progressiveMauve binary, and have made it available here: > > http://gel.ahabs.wisc.edu/mauve/downloads/progressiveMauve_2.1.1_linux_x64.gz > > > > simply download, gunzip, and replace the original 64-bit > > progressiveMauve. > > > > > > Regards, > > -Aaron > > > > > > On Fri, 2008-02-22 at 16:52 -0800, Morgan Langille wrote: > > > > > I am trying to aligning 13 pseudomonas genomes, but I am having some > > > problems. I first tried this on a 4GB 32 bit machine and received out of > > > memory errors. I then tried running the 64 bit version of > > > progressiveMauve on a 64 bit machine with 16GB memory (dual quad core > > > Xeon processor) and I get the error below. Regular mauveAligner (64 bit > > > version) works without any problems. I also tried running it with the > > > --disable-cache option and still received the same error. Note that the > > > process does not actually end, but just stays there "waiting" (I waited > > > 4 hours at least before killing it). > > > > > > Any suggestions? > > > > > > Morgan > > > > > > > > > > > > Sequence loaded successfully. > > > NC_002516.gbk 6264404 base pairs. > > > Sequence loaded successfully. > > > NC_002947.gbk 6181863 base pairs. > > > Sequence loaded successfully. > > > NC_004129.gbk 7074893 base pairs. > > > Sequence loaded successfully. > > > NC_004578.gbk 6397126 base pairs. > > > Sequence loaded successfully. > > > NC_005773.gbk 5928787 base pairs. > > > Sequence loaded successfully. > > > NC_007005.gbk 6093698 base pairs. > > > Sequence loaded successfully. > > > NC_007492.gbk 6438405 base pairs. > > > Sequence loaded successfully. > > > NC_008027.gbk 5888780 base pairs. > > > Sequence loaded successfully. > > > NC_008463.gbk 6537648 base pairs. > > > Sequence loaded successfully. > > > NC_009434.gbk 4567418 base pairs. > > > Sequence loaded successfully. > > > NC_009439.gbk 5072807 base pairs. > > > Sequence loaded successfully. > > > NC_009512.gbk 5959964 base pairs. > > > Sequence loaded successfully. > > > NC_009656.gbk 6588339 base pairs. > > > Using weight 15 mers for initial seeds > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 2 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 seconds. > > > Creating sorted mer list > > > Create time was: 4 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. > > > waiting > > > > > > > > > > > > ------------------------------------------------------------------------- > > 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
