Hello Robert, some responses below...
Ingraham, Robert wrote: > > I am trying run mauve using a Linux platform, it ‘hangs up” after > about 15 minutes. This is my fifth attempt, is there anything obvious > I am doing wrong? > > I am using a FASTA multi file as input. > > This is the command line file: > <snip> > > /share/apps/mauve/mauve_2.1.1/linux-x64/progressiveMauve --seed-family > --seed-weight=19 --output=/home/RGIngraham/Clostridia_10a > --backbone-output=/home/RGIngraham/Clostridia_10a.backbone > --output-guide-tree=/home/RGIngraham/Clostridia_10a.guide_tree > /home/RGIngraham/Clostridia_10.mfa.txt > > This is the output: > <snip> > 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 > > waiting > The "indefinite waiting" phenomenon was a bug specific to the linux 64-bit build of progressiveMauve 2.1.1. For reference, this bug was also described in the following mailing list thread: http://www.mail-archive.com/[email protected]/msg00035.html Until a new progressiveMauve release can be made, the best workaround for 64-bit linux is to use the 2.0.0 build available here: http://gel.ahabs.wisc.edu/mauve/downloads/misc/progressiveMauve_2.0.0_linux_x64_ghostfix.tar.gz Another hint is that you will need to remove the --seed-family option as it was introduced in 2.1.0 and thus is not compatible with the 2.0.0 release. Hope that helps, -Aaron ------------------------------------------------------------------------- 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
