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<mailto:gmarg...@gmail.com>
gabriele.mar...@lgl.bayern.de<mailto: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<mailto: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<file:///\\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<file:///\\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<mailto:gmarg...@gmail.com>
gabriele.mar...@lgl.bayern.de<mailto: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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