Hi Brianna, as you noted in your following e-mail, the alignment eventually finished. The delay at that stage is normal for sequences of the size you were aligning, and the aligner does not produce any output during that stage (which involves removal of spurious alignments using a Homology HMM, as described in the progressiveMauve manuscript).
As for parallelism via multithreading, it is possible in theory but would require modifying the aligner code appropriately using e.g. OpenMP directives, taking care to ensure use of static variables & any shared datastructures are handled appropriately across threads. Best, -Aaron On Tue, 2013-09-17 at 08:05 +1000, Brianna Flynn wrote: > Hi there, > I'm using progressive Mauve to align a draft genome (~2.8 Gbp) to the > mouse mm10 build (also ~2.8Gbp). Downloading the snapshot update of > version 2.3.1 definitely helped get the alignment past the point of > error that I was previously encountering. I have at my disposal a > computer with more than enough memory to accommodate this, but the > alignment as it stands has already been running for over 72 hours. The > last update shown on the Mauve console is as follows: > > > Performing final pass iterative refinement > > > 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%.. > 100%..Fix left ends > > > done. > root alignment has 85351 superintervals > root alignment length: 3971048854 > > > The computer still shows that progressiveMauve is running, but there > has been no update to any of the files or the Mauve Console for ~8hrs. > My first question is whether or not this is normal? I just want to > make sure something hasn't gone wrong before I let it continue > running. My second question is whether or not I can split up my fast > files and run multiple threads at once, then combine these at the end > to speed up the process? My IT guru tells me our computer has enough > memory to do this, but it's just whether or not the program will allow > this and/or if the alignment could be compromised in some way by doing > this. > > > Thanks for all the help. > > > Cheers, > Brianna Flynn -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
