Hi Ray, thanks for the extra details. It should be fine to provide sequences in a single input file to progressiveMauve, but xmfa2maf hasn't been tested with that kind of input and I don't think it will work. In this case can you try splitting your sequences out into separate files prior to alignment with progressiveMauve? You are right that if each file only contains a single sequence that this error condition (and message which has a typo!) should not be popping up. So please let me know if it's not working after the sequences have been split into individual files.
Best, -Aaron On Mon, 2014-05-26 at 23:07 +0800, Raymond Wan wrote: > 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 -- 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
