Sounds like there is something unusual in one of your plasmid
sequences. It should take less than a minute to align a pair of
Borrelia-sized genomes, even with plasmids included. If you can send
the zipped genomes with plasmids to my personal email (off-list) I can
investigate further.
Best,
-Aaron
On Tue, 2017-04-11 at 14:26 +0000, gabriele.mar...@lgl.bayern.de wrote:
> Dear Aaron,
> thank you very much for the quick response. I will try that. I have
> to say that if I use only the main chromosome for the reference, the
> alignment works. So, perhaps I should explain that these are Borrelia
> genomes that I would like to align and they consist of a main
> chromosome and about 10 plasmids. If I use only the chromosom
> sequence, everything works fine. Just if I try to align the two
> complete genomes, I get this message. There is no other error
> message.
> I copied the files on my computer and started from there but the same
> happened again. Checking task manager, I can see javaw.exe but
> nothing seems to happen. However, when I try to close the window, it
> tells me that there is an alignment in progress and closing it would
> terminate the process. Is it possible that it just takes such a long
> time?
> Kind regards,
> Gabi
>
> Gabriele Margos
> German National Reference Centre for Borrelia
> Bavarian Health and Food Safety Authority
> Veterinärstrasse 2
> 85764 Oberschleißheim
> Tel. 09131/68085883
> email:
> gmarg...@gmail.com
> gabriele.mar...@lgl.bayern.de
>
>
> Von: Aaron Darling [mailto:aaron.darl...@uts.edu.au]
> Gesendet: Dienstag, 11. April 2017 11:28
> An: mauve-users@lists.sourceforge.net
> Betreff: Re: [Mauve-users] Mauve alignment not running
>
> Hi Gabriele,
> First suggestion, try copying the sequence files from your file
> server over to the local disk (C:) and running the alignment, in
> order to rule out a network file access problem.
> If that fails, can you tell us what version of windows you are using,
> and also whether progressiveMauve.exe appears in the windows task
> manager when you run it?
> And was there any other error message that popped up? If not, can you
> try aligning the two files on another computer with a different OS
> (eg Mac) or version of Windows?
> Best,
> -Aaron
>
> On Tue, 2017-04-11 at 07:37 +0000, gabriele.mar...@lgl.bayern.de
> wrote:
> Hi, I tried to make an alignment in Mauve using two fasta files. The
> alignment did not run but I got the following message:
>
> OS name is: Windows 7 arch: amd64
> Executing:
> win64\progressiveMauve --output=\\umwelt.bayern.de\LGL-
> Users\Home\OS_L-Z\Margos_G\Dokumente\Bob Lane\CA690\Mauve
> CA690\PKo_CA690_genome_align\DN127_CA690 --output-guide-
> tree=\\umwelt.bayern.de\LGL-Users\Home\OS_L-Z\Margos_G\Dokumente\Bob
> Lane\CA690\Mauve CA690\PKo_CA690_genome_align\DN127_CA690.guide_tree
> --backbone-output=\\umwelt.bayern.de\LGL-Users\Home\OS_L-
> Z\Margos_G\Dokumente\Bob Lane\CA690\Mauve
> CA690\PKo_CA690_genome_align\DN127_CA690.backbone
> \\umwelt.bayern.de\LGL-Users\Home\OS_L-Z\Margos_G\Dokumente\Bob
> Lane\CA690\Mauve CA690\Bbis_DN127_complete_genome_reord.fasta
> \\umwelt.bayern.de\LGL-Users\Home\OS_L-Z\Margos_G\Dokumente\Bob
> Lane\CA690\Mauve CA690\CA690_DJ_spades_contigs_1000.fasta
>
> What can I do?
>
> Gabriele Margos
>
> Gabriele Margos
> German National Reference Centre for Borrelia
> Bavarian Health and Food Safety Authority
> Veterinärstrasse 2
> 85764 Oberschleißheim
> Tel. 09131/68085883
> email:
> gmarg...@gmail.com
> gabriele.mar...@lgl.bayern.de
>
>
>
> --
> Aaron E. Darling, Ph.D.
> Associate Professor, ithree institute
> University of Technology Sydney
> Australia
>
> http://darlinglab.org
> twitter: @koadman
>
>
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--
Aaron E. Darling, Ph.D.
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University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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