Re: [Mauve-users] XMFA TO MAF

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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 <aar...@ut...>:

> 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 <aar...@ut...>:
>
> 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 <aar...@ut...>:
>
> 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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> University of Technology Sydney
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> twitter: @koadman
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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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