Hi Aaron, Thank you for your reply!
I see. I'm wondering if I'm doing something wrong since I am aligning a set of sequences with each other. Your explanation seems to imply that maybe I have one sequence aligning across two sequences, which is not what I want. That is, if I have 3 sequences x1, x2, and x3, I want each one to align with the other two. I don't want part of x1 to span across x2 and x3. Am I running Mauve incorrectly? I concatenated all of the sequences into a single file and fed them into Mauve ... perhaps that was the wrong thing to do? Thank you for your help! Ray PS: I guess it would be more correct for the error message to say "must not" instead of "must"? Quoting Aaron Darling <aaron.darl...@uts.edu.au>: > Hi Ray, > As the error states, xmfa2maf does not support alignments that span > multiple contigs or chromosomes. This would be a nice feature to have > but isn't exactly trivial to implement. One workaround might be to > concatenate all of your sequences prior to alignment, although that may > complicate whatever you plan to do next with the MAF. > > Best, > -Aaron > > On Fri, 2014-05-16 at 17:53 +1000, Raymond Wan wrote: > > Dear all, > > > > I am getting a strange error when I use xmfa2maf (downloaded from the > > "All other programs" link). My original FASTA file has a set of > > sequences. After they are all loaded (i.e., various "Sequence loaded > > successfully." messages), I get this error: > > > > interval 20 seq 1 left 1033547 right 1038442 > > l_baseI 1033547 r_baseI 128 l_contigI 0 r_contigI 1 name ... > > Error, input alignment must spans multiple contigs/chromosomes. Unable > > to translate to MAF > > > > Has anyone encountered this error before? Thank you in advance! > > > > Ray > > > > PS: I had asked an unrelated question back on May 2nd about the format > > of the SNP file. If someone could help me out with that, that would be > > great! I'm actually still unsure of the file format... > > > > > > > ------------------------------------------------------------------------------ > > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > > Instantly run your Selenium tests across 300+ browser/OS combos. > > Get unparalleled scalability from the best Selenium testing platform > available > > Simple to use. Nothing to install. Get started now for free." > > http://p.sf.net/sfu/SauceLabs > > _______________________________________________ > > Mauve-users mailing list > > Mauve-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/mauve-users > > -- > 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. > > ------------------------------------------------------------------------------ > The best possible search technologies are now affordable for all companies. > Download your FREE open source Enterprise Search Engine today! > Our experts will assist you in its installation for $59/mo, no commitment. > Test it for FREE on our Cloud platform anytime! > http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users > > ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk ------------------------------------------------------------------------------ The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
