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
