Dear all,
I am using mauve contig mover through command line .I have a question:
once i am running mauve contig mover i am getting n number iteration for
each run and for each run mauve generate one folder name alignment1,
alignment2.....alignmentN . Now i want only final iteration result, from
command line after running mauve how i will automatically go to that folder
and pass the result to another folder in different location.
Regards
Hiren
On 16 July 2013 08:52, Aaron Darling <[email protected]> wrote:
>
> Hello Hiren, (reply below)
>
> On Tue, 2013-07-09 at 16:59 +0200, Hiren Ghosh wrote:
> > Dear All, I used MIRA for genome assembly and i got contigfile "
> > Ecoli-1_out.unpadded.fasta". Now i want to do alignment with this
> > contig with another Ecoli genome " refseq.fasta". In command line i am
> > typinglike this and getting error message.
> > Attempt 1: ./mauveAligner --output=ec_ec.mauve
> > --output-alignment=ec_vs_ec.alignment Ecoli-1_out.unpadded.fasta
> > refseq.fasta Sequence loaded successfully. Ecoli-1_out.unpadded.fasta
> > 4982364 base pairs. Using weight 15 mers for initial seeds Creating
> > sorted mer list Create time was: 2 seconds.
> > 0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%..
> > 11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
> > 21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
> > 31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
> > 41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
> > 51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
> > 61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
> > 71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
> > 81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
> > 91%..92%..93%..94%..95%..96%..97%..98%..99%..Starting with 0 MUMs
> > Eliminating overlaps yields 0 MUMs
>
> In this case, mauveAligner was unable to find any exact matches of
> length 15 or greater among your input sequences. This generally happens
> when the genomes are too divergent to be aligned at the nucleotide
> level. Unless you want mauveAligner for some historical reason, I
> suggest you use progressiveMauve if possible since it can align more
> divergent genomes than mauveAligner and is generally more accurate.
> However, if mauveAligner couldn't find any matches at all,
> progressiveMauve will probably not do much better. Check that your
> refseq input file does in fact contain sequence data -- there was only
> one message in the output above giving the sequence size but that is
> usually printed for both sequences.
>
>
> > Attempt2: ./mauveAligner --output=jb50vsSpmito.mauve
> > --output-alignment=jb50vsSpmito.alignment Ecoli-1_out.unpadded.fasta
> > jb50contigs.fa.sslist refseq.fasta Sp.may2011.extras_mito.fasta.sslist
> > Sequence loaded successfully. Ecoli-1_out.unpadded.fasta 4982364 base
> > pairs. Sequence loaded successfully. refseq.fasta 2435000 base pairs.
> > Using weight 15 mers for initial seeds Creating sorted mer list Create
> > time was: 2 seconds. Creating sorted mer list ERROR! gap character
> > encountered at genome sequence position 61 Input sequences must be
> > unaligned and ungapped!
>
> Unlike many errors generated by Mauve, this error message is pretty
> self-explanatory. There is some kind of non-nucleotide character in your
> input sequence. I think MIRA assembler output includes non-nucleotide
> characters in some cases. Check the MIRA documentation and fix your
> input files accordingly.
>
> Best,
> -Aaron
>
> --
> Aaron E. Darling, Ph.D.
> Associate Professor, ithree institute
> University of Technology Sydney
> Australia
>
> http://darlinglab.org
> twitter: @koadman
>
>
>
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--
*Hiren Ghosh, Doctoral Research Scholar *
*Biomedizinisches Forschungszentrum Seltersberg
Institut für Medizinische Mikrobiologie
Justus-Liebig-Universität
Schubertstr. 81
35392 Gießen , Germany
*
*Mobile No: 017672157634
*
*Email:[email protected]*
.
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