I see. It looks like you've got some large assemblies that are likely
to be multichromosomal and possibly in multiple contigs.
Unfortunately xmfa2maf only supports finished unichromosomal
assemblies.
Depending on what you intend to do next you might be able to get a
hackish solution by simply concatenating all of the contigs in those
genomes before assembling with progressiveMauve.
But if you need the contig information that won't work obviously and I
can't offer an easy solution right now.
-Aaron
On Wed, 2017-02-01 at 10:41 +0100, ait zai Lynda wrote:
> Hi Aaron, i executed the xmfa2tomaf in the original locations, it
> doesn't work completely.
> i don't know what i must edit in the .xmfa file. May be i must masque
> first the repeated sequences of the genomes before progressiveMauve
> ?
>
> Here what i did:
>
> $ ./xmfa2maf threeway.xmfa threeway.maf
> Sequence loaded successfully.
> Pol1_final_sorted.fasta 52638403 base pairs.
> Sequence loaded successfully.
> Polytomella_capuana_v1_id8.fasta 80325395 base pairs.
> Sequence loaded successfully.
> Polytomella_magna_v1_id8.fasta 68237959 base pairs.
> Sequence loaded successfully.
> Polytomella_parva_v1_id8.fasta 46970636 base pairs.
> Sequence loaded successfully.
> Polytomella_piriformis_v1_id8.fasta 47387763 base pairs.
> interval 108 seq 3 left 45472019 right 45472019
> l_baseI 1 r_baseI 5917 l_contigI 5831 r_contigI 5830 name
> Pparva_contig_5832_cov_64_99 db=Polytomella_parva_v1_id8
> Error, input alignment spans multiple contigs/chromosomes. Unable to
> translate to MAF
>
>
>
> 2017-01-31 23:24 GMT+01:00 Aaron Darling <aaron.darl...@uts.edu.au>:
> > Hi Lynda, xmfa2maf needs to read the sequence files that went into
> > threeway.xmfa, and the "FileNotOpened" exception is probably
> > happening because they are no longer accessible at the original
> > paths stored in the xmfa. There are a few options:
> > 1) restore the sequence files and the xmfa to their original
> > locations and run xmfa2maf from there
> > 2) edit threeway.xmfa to point to the current file paths to the
> > sequence files
> > 3) re-run the genome alignment, then run xmfa2maf on the resulting
> > xmfa
> >
> >
> >
> > On Tue, 2017-01-31 at 21:29 +0100, ait zai Lynda wrote:
> > > Hi Aaron, Thank you for your answer.
> > >
> > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well.
> > > But when i try to execute i get this results :
> > >
> > > $./xmfa2maf threeway.xmfa threeway.maf
> > >
> > > Exception FileNotOpened thrown from
> > > Unknown() in gnFileSource.cpp 67
> > > Called by Unknown()
> > > Segmentation fault (core dumped)
> > >
> > > Would you know how to do to execute the xmaf2maf proprly?
> > >
> > >
> > > Thank you fore your help :)
> > >
> > > 2017-01-31 21:21 GMT+01:00 Aaron Darling
> > > u>:
> > > > Hi Lynda, can you please reply on list instead of privately?
> > > >
> > > > On Tue, 2017-01-31 at 17:12 +0100, ait zai Lynda wrote:
> > > > > Hi Aaron, Thank you for your answer.
> > > > >
> > > > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well.
> > > > > But when i try to execute i get this results :
> > > > >
> > > > > $./xmfa2maf threeway.xmfa threeway.maf
> > > > >
> > > > > Exception FileNotOpened thrown from
> > > > > Unknown() in gnFileSource.cpp 67
> > > > > Called by Unknown()
> > > > > Segmentation fault (core dumped)
> > > > >
> > > > > Would you know how to do to execute the xmaf2maf proprly?
> > > > >
> > > > >
> > > > > Thank you fore your help :)
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > 2017-01-30 2:35 GMT+01:00 Aaron Darling
> > > > > u.au>:
> > > > > > Hi Lynda, have you tried using the xmfa2maf program that is
> > > > > > part of the Mauve codebase? A build for linux is available
> > > > > > here:
> > > > > > http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux
> > > > > > -x64/xmfa2maf.bz2
> > > > > >
> > > > > > to run one must first do:
> > > > > > bunzip2 xmfa2maf
> > > > > > chmod 755 xmfa2maf
> > > > > >
> > > > > > If you've already tried that without luck can you describe
> > > > > > the problems you encountered?
> > > > > >
> > > > > > Cheers,
> > > > > > -Aaron
> > > > > >
> > > > > > On Sun, 2017-01-29 at 16:37 +0100, ait zai Lynda wrote:
> > > > > > > hi everyone,
> > > > > > >
> > > > > > > i'm new in the alignment, i want to convert my XMFA file
> > > > > > > to MAF file.
> > > > > > > Does anyone know how i can do it?
> > > > > > >
> > > > > > >
> > > > > > > thank you in advance
> > > > > > > -------------------------------------------------------
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Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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