Hi Aaron, Thanks for the suggestion. Yes, my input is a set of bacterial genomes.
I re-ran progressiveMauve last night and gave xmfa2maf a try and yes, providing the sequences on the command line instead of a single concatenated file worked! No more error messages from xmfa2maf! Thank you very much for your help! Never would have thought of that... Ray On 2014-05-27 08:31, Aaron Darling wrote: > 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. 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