Thread: [Mauve-users] Mauve alignment not running
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From: <Gab...@lg...> - 2017-04-11 07:37:11
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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: gma...@gm...<mailto:gma...@gm...> gab...@lg...<mailto:gab...@lg...> |
From: Aaron D. <aar...@ut...> - 2017-04-11 09:28:16
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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, Gab...@lg... 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: > gma...@gm... > gab...@lg... > > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
From: <Gab...@lg...> - 2017-04-11 14:26:46
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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: gma...@gm...<mailto:gma...@gm...> gab...@lg...<mailto:gab...@lg...> Von: Aaron Darling [mailto:aar...@ut...] Gesendet: Dienstag, 11. April 2017 11:28 An: mau...@li... 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, Gab...@lg...<mailto:Gab...@lg...> 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: gma...@gm...<mailto:gma...@gm...> gab...@lg...<mailto:gab...@lg...> -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman ________________________________ UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
From: Aaron D. <aar...@ut...> - 2017-04-11 21:11:25
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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, Gab...@lg... 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: > gma...@gm... > gab...@lg... > > > Von: Aaron Darling [mailto:aar...@ut...] > Gesendet: Dienstag, 11. April 2017 11:28 > An: mau...@li... > 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, Gab...@lg... > 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: > gma...@gm... > gab...@lg... > > > > -- > Aaron E. Darling, Ph.D. > Associate Professor, ithree institute > University of Technology Sydney > Australia > > http://darlinglab.org > twitter: @koadman > > > UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and > any accompanying attachments may contain confidential information. If > you are not the intended recipient, do not read, use, disseminate, > distribute or copy this message or attachments. If you have received > this message in error, please notify the sender immediately and > delete this message. Any views expressed in this message are those of > the individual sender, except where the sender expressly, and with > authority, states them to be the views of the University of > Technology Sydney. Before opening any attachments, please check them > for viruses and defects. Think. Green. Do. Please consider the > environment before printing this email. -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |