mauve-users Mailing List for Mauve (Page 3)
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From: Thierry K.S. J. <t.k...@vu...> - 2016-10-12 15:09:42
|
Dear Dr. Darling/Aaron, I have a small question regarding the interpretation of the coordinates in the exported gap file. The headers in this tab delimited file is less than the nuber of colums. This makes the interpretation cumbersome. Could you also give a hint how to maintain the annotations in from the Genbank, beyond the first iteration of the contig reordering? Thank you in advance for a short explanation on this. kind regards, Thierry Janssens |
From: Karla P. <kar...@gm...> - 2016-10-07 15:14:19
|
Dear all, I'm struggling in a Mauve analysis and wonder if someone could help me. I'm studying 13 genomes from diff bacteria and I performed a progressiveMauve alignment from the graphical interface using the last version of Mauve snapshot for Linux (2015-02-13). I have as output the follow files: 1. no extension (I use to open the graphical interface); 2. .backbone; 3. .bbcols ; 4. .guide_tree. I would like to have the coordinates from LCBs, since I have multiple genomes and they have up to 900 scaffolds. As example, I would like to an output such as: scaffold start end genome strand * NZ_KB902575.1 1695199 1695311 - * I checked in the list and saw an answer from Aaron about xmfa2maf but, since I don't have a .xmfa file I tried it but I got a kinda NT file that does not have every LCB. Does anyone know how can I get what I'm looking for? Thank you in advance. Best, Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=kar...@gm...&idSignature=22> [image: photo] *Karla Pollyanna Vieira de Oliveira* Biologist / MSc. Bioinformatics, Laboratório de Tecnologias Integradas (InteLab) +55 48 9133-9078 | +55 31 987-677-667 | kar...@gm... | ka...@in... | Skype: karla_pollyanna <#> <http://facebook.com/karla.biotecnologia> <http://us.linkedin.com/in/karla-oliveira-a438a336> Get a signature like this: Click here! <http://ws-promos.appspot.com/r?rdata=eyJydXJsIjogImh0dHA6Ly93d3cud2lzZXN0YW1wLmNvbS9lbWFpbC1pbnN0YWxsP3dzX25jaWQ9NjcyMjk0MDA4JnV0bV9zb3VyY2U9ZXh0ZW5zaW9uJnV0bV9tZWRpdW09ZW1haWwmdXRtX2NhbXBhaWduPXByb21vXzU3MzI1Njg1NDg3Njk3OTIiLCAiZSI6ICI1NzMyNTY4NTQ4NzY5NzkyIn0=&u=501424197656821> |
From: Aaron D. <aar...@ut...> - 2016-10-07 11:50:30
|
Hi Shlomo, The short answer is probably not, because progressiveMauve is unlikely to scale to > 100 bacterial genomes. Might be ok for small viruses. You might try the harvest tools by Todd Treangen & colleagues: http://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html It computes only a core genome alignment but that may be enough to extract the phylogenetic signal of interest. There are a range of read-mapping to reference genome based approaches but I won't comment on those here. Best, -Aaron On Wed, 2016-10-05 at 13:21 +0300, Shlomo Blum wrote: > Hi Aaron, > > Would this be also a good option for > 100 genomes? > > > On Tue, Oct 4, 2016 at 4:39 PM, Aaron Darling > au> wrote: > > Hi Michael, I realize this is coming late, but still want to post a > > reply for the benefit of others who may be curious in the future. > > There are a number of ways to generate phylogenies from genome > > alignments. If you want to use Mauve I suggest doing the alignment > > with progressiveMauve then extracting the core genome alignment > > blocks with stripSubsetLCBs. From that point you could use > > ClonalFrameML or another alternative. There are some example > > instructions for these steps (and beyond that) on this page: > > https://github.com/xavierdidelot/ClonalOrigin/wiki/Usage > > > > > > On Fri, 2016-08-19 at 08:27 +0000, mic...@ag...min.c > > h wrote: > > > I am looking for a way to generate a phylogenetic tree of 30 > > > pseudomonas strains by using mauve. Since the guidetree outputted > > > by progressiveMauve is not a "real" phylogenetic tree I am > > > looking for another "whole genome approach". > > > > > > Would it be an option to generate a phylogenetic tree the > > > following way?: > > > 1. Get FastA file form 30 strains and concatenate into one file > > > 2. Align them with command: mauveAligner --output=ps.mauve.phylip > > > --output-alignment=ps.alignment.phylip --weight=300 --alignment- > > > output-format=phylip --alignment-output-dir=. ../ > > > inp/all/all.fasta > > > 3. Use raxml or fastree on the phylip which gets generated by > > > mauveAligner > > > > > > Thx > > > Michael > > > > > > --------------------------------------------------------------- > > > --------------- > > > _______________________________________________ > > > Mauve-users mailing list > > > Mau...@li... > > > https://lists.sourceforge.net/lists/listinfo/mauve-users > > -- > > 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. > > > > ----------------------------------------------------------------- > > ------------- > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > _______________________________________________ > > Mauve-users mailing list > > Mau...@li... > > https://lists.sourceforge.net/lists/listinfo/mauve-users > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- 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: Chaib De M. M. <m.c...@ru...> - 2016-10-05 13:02:34
|
Yes, it did. Thank you very much! On Wed, Oct 5, 2016 at 2:57 PM, Guy Plunkett III <guy...@wi...> wrote: > Hi Maryam, > > This is a clue: > > FileNotFoundException: C:\Users\p270270\Desktop\ > CompGenTutorial\NC_011748.fna\NC_011748.fna (The system cannot find the > path specified) > > > When using the GUI interface (on either Windows or MacOS) as opposed to > command line, I have discovered that if you double-click on the file name > after navigating to it in the interface, the file name is occasionally used > as both a directory name and a file name. Single click to select, and then > click on the Open button. This happens to me more often with .gbk files, or > fasta files with extensions other than .fas or .fasta, so it might reflect > some underlying assumption about file names … > > Any way, try that and see if it solves your issue. > > Cheers, > Guy > > Dr. Guy Plunkett III > Senior Scientist Emeritus, University of Wisconsin-Madison > Senior Scientist, DNASTAR, Inc. > http://www.genome.wisc.edu/information/gplunkett.html > > > > On Oct 5, 2016, at 1:37 AM, Chaib De Mares, M. <m.c...@ru...> > wrote: > > Hello, > > I am new to this list, and I don't know whether this has been asked > before. I apologize before hand if there's duplication. > When I try to upload my reference and then draft genome to Mauve, I get an > error saying that java cannot bind my document to parent. I am running the > latest JRE version (8u102) on a 64-bit Windows computer. I understand that > it should work, because Mauve can work on 1.4 or later. > Could you please point out what could be the issue? > > See details below: > > Thank you! > Maryam > > ------- > shown > Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to > bind C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna to parent > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown > Source) > at sun.awt.shell.ShellFolder.invoke(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at java.util.concurrent.FutureTask.run(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown > Source) > at java.lang.Thread.run(Unknown Source) > Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to > bind C:\Users\p270270\Desktop\CompGenTutorial\SRR292770_unordered.fasta > to parent > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown > Source) > at sun.awt.shell.ShellFolder.invoke(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at java.util.concurrent.FutureTask.run(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown > Source) > at java.lang.Thread.run(Unknown Source) > Copying... > C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna > to > C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\ > alignment1\NC_011748.fna > java.io.FileNotFoundException: C:\Users\p270270\Desktop\ > CompGenTutorial\NC_011748.fna\NC_011748.fna (The system cannot find the > path specified) > at java.io.FileInputStream.open0(Native Method) > at java.io.FileInputStream.open(Unknown Source) > at java.io.FileInputStream.<init>(Unknown Source) > at org.gel.air.util.IOUtils.copyFile(Unknown Source) > at org.gel.mauve.contigs.ContigOrderer.copyInputFiles(Unknown Source) > at org.gel.mauve.contigs.ContigMauveAlignFrame. > alignButtonActionPerformed(Unknown Source) > at org.gel.mauve.gui.AlignFrame$9.actionPerformed(Unknown Source) > at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown > Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEventImpl(Unknown Source) > at java.awt.EventQueue.access$500(Unknown Source) > at java.awt.EventQueue$3.run(Unknown Source) > at java.awt.EventQueue$3.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.ProtectionDomain$JavaSecurityAccessImpl. > doIntersectionPrivilege(Unknown Source) > at java.security.ProtectionDomain$JavaSecurityAccessImpl. > doIntersectionPrivilege(Unknown Source) > at java.awt.EventQueue$4.run(Unknown Source) > at java.awt.EventQueue$4.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.ProtectionDomain$JavaSecurityAccessImpl. > doIntersectionPrivilege(Unknown Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.run(Unknown Source) > Running alignment. > Executing > win64\progressiveMauve > --output=C:\Users\p270270\Desktop\CompGenTutorial\ > MauveOutput\alignment1\alignment1 > --skip-refinement > --weight=200 > --output-guide-tree=C:\Users\p270270\Desktop\ > CompGenTutorial\MauveOutput\alignment1\alignment1.guide_tree > --backbone-output=C:\Users\p270270\Desktop\ > CompGenTutorial\MauveOutput\alignment1\alignment1.backbone > C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna > C:\Users\p270270\Desktop\CompGenTutorial\SRR292770_ > unordered.fasta\SRR292770_unordered.fasta > Exception FileNotOpened thrown from > Unknown() in ..\libGenome\gnFileSource.cpp 67 > Called by Unknown() > Exited with error code: -1073741676 > -- > Maryam Chaib De Mares > M.Sc. Evolutionary Biology > PhD Candidate - Microbial Ecology Department > Groningen Institute for Evolutionary Life Sciences (GELIFES) > Rijksuniversiteit Groningen > Nijenborgh 7, 9747 AG Groningen > Linnaeusborg, room 0766 > +31 50 363 2169 > m.c...@ru... > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot______ > _________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > > > -- -- Maryam Chaib De Mares M.Sc. Evolutionary Biology PhD Candidate - Microbial Ecology Department Groningen Institute for Evolutionary Life Sciences (GELIFES) Rijksuniversiteit Groningen Nijenborgh 7, 9747 AG Groningen Linnaeusborg, room 0766 +31 50 363 2169 m.c...@ru... |
From: Guy P. I. <guy...@wi...> - 2016-10-05 12:57:58
|
Hi Maryam, This is a clue: > FileNotFoundException: C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna (The system cannot find the path specified) When using the GUI interface (on either Windows or MacOS) as opposed to command line, I have discovered that if you double-click on the file name after navigating to it in the interface, the file name is occasionally used as both a directory name and a file name. Single click to select, and then click on the Open button. This happens to me more often with .gbk files, or fasta files with extensions other than .fas or .fasta, so it might reflect some underlying assumption about file names … Any way, try that and see if it solves your issue. Cheers, Guy Dr. Guy Plunkett III Senior Scientist Emeritus, University of Wisconsin-Madison Senior Scientist, DNASTAR, Inc. http://www.genome.wisc.edu/information/gplunkett.html On Oct 5, 2016, at 1:37 AM, Chaib De Mares, M. <m.c...@ru...> wrote: > Hello, > > I am new to this list, and I don't know whether this has been asked before. I apologize before hand if there's duplication. > When I try to upload my reference and then draft genome to Mauve, I get an error saying that java cannot bind my document to parent. I am running the latest JRE version (8u102) on a 64-bit Windows computer. I understand that it should work, because Mauve can work on 1.4 or later. > Could you please point out what could be the issue? > > See details below: > > Thank you! > Maryam > > ------- > shown > Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to bind C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna to parent > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown Source) > at sun.awt.shell.ShellFolder.invoke(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at java.util.concurrent.FutureTask.run(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) > Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to bind C:\Users\p270270\Desktop\CompGenTutorial\SRR292770_unordered.fasta to parent > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown Source) > at sun.awt.shell.ShellFolder.invoke(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source) > at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) > at java.util.concurrent.FutureTask.run(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) > at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) > Copying... > C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna > to > C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\NC_011748.fna > java.io.FileNotFoundException: C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna (The system cannot find the path specified) > at java.io.FileInputStream.open0(Native Method) > at java.io.FileInputStream.open(Unknown Source) > at java.io.FileInputStream.<init>(Unknown Source) > at org.gel.air.util.IOUtils.copyFile(Unknown Source) > at org.gel.mauve.contigs.ContigOrderer.copyInputFiles(Unknown Source) > at org.gel.mauve.contigs.ContigMauveAlignFrame.alignButtonActionPerformed(Unknown Source) > at org.gel.mauve.gui.AlignFrame$9.actionPerformed(Unknown Source) > at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEventImpl(Unknown Source) > at java.awt.EventQueue.access$500(Unknown Source) > at java.awt.EventQueue$3.run(Unknown Source) > at java.awt.EventQueue$3.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) > at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) > at java.awt.EventQueue$4.run(Unknown Source) > at java.awt.EventQueue$4.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.run(Unknown Source) > Running alignment. > Executing > win64\progressiveMauve > --output=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1 > --skip-refinement > --weight=200 > --output-guide-tree=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1.guide_tree > --backbone-output=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1.backbone > C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna > C:\Users\p270270\Desktop\CompGenTutorial\SRR292770_unordered.fasta\SRR292770_unordered.fasta > Exception FileNotOpened thrown from > Unknown() in ..\libGenome\gnFileSource.cpp 67 > Called by Unknown() > Exited with error code: -1073741676 > -- > Maryam Chaib De Mares > M.Sc. Evolutionary Biology > PhD Candidate - Microbial Ecology Department > Groningen Institute for Evolutionary Life Sciences (GELIFES) > Rijksuniversiteit Groningen > Nijenborgh 7, 9747 AG Groningen > Linnaeusborg, room 0766 > +31 50 363 2169 > m.c...@ru... > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Shlomo B. <shl...@ma...> - 2016-10-05 10:50:41
|
Hi Aaron, Would this be also a good option for > 100 genomes? On Tue, Oct 4, 2016 at 4:39 PM, Aaron Darling <aar...@ut...> wrote: > Hi Michael, I realize this is coming late, but still want to post a reply > for the benefit of others who may be curious in the future. > There are a number of ways to generate phylogenies from genome alignments. > If you want to use Mauve I suggest doing the alignment with > progressiveMauve then extracting the core genome alignment blocks with > stripSubsetLCBs. From that point you could use ClonalFrameML or another > alternative. There are some example instructions for these steps (and > beyond that) on this page: > https://github.com/xavierdidelot/ClonalOrigin/wiki/Usage > > > On Fri, 2016-08-19 at 08:27 +0000, mic...@ag... > wrote: > > I am looking for a way to generate a phylogenetic tree of 30 pseudomonas strains by using mauve. Since the guidetree outputted by progressiveMauve is not a "real" phylogenetic tree I am looking for another "whole genome approach". > > Would it be an option to generate a phylogenetic tree the following way?: > 1. Get FastA file form 30 strains and concatenate into one file > 2. Align them with command: mauveAligner --output=ps.mauve.phylip --output-alignment=ps.alignment.phylip --weight=300 --alignment-output-format=phylip --alignment-output-dir=. ../ inp/all/all.fasta > 3. Use raxml or fastree on the phylip which gets generated by mauveAligner > > Thx > Michael > > ------------------------------------------------------------------------------ > _______________________________________________ > Mauve-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/mauve-users > > -- > 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. > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > > |
From: Chaib De M. M. <m.c...@ru...> - 2016-10-05 07:20:35
|
Hello, I am new to this list, and I don't know whether this has been asked before. I apologize before hand if there's duplication. When I try to upload my reference and then draft genome to Mauve, I get an error saying that java cannot bind my document to parent. I am running the latest JRE version (8u102) on a 64-bit Windows computer. I understand that it should work, because Mauve can work on 1.4 or later. Could you please point out what could be the issue? See details below: Thank you! Maryam ------- shown Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to bind C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna to parent at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown Source) at sun.awt.shell.ShellFolder.invoke(Unknown Source) at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source) at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source) at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to bind C:\Users\p270270\Desktop\CompGenTutorial\SRR292770_unordered.fasta to parent at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source) at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown Source) at sun.awt.shell.ShellFolder.invoke(Unknown Source) at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source) at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source) at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Copying... C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna to C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\NC_011748.fna java.io.FileNotFoundException: C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna (The system cannot find the path specified) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(Unknown Source) at java.io.FileInputStream.<init>(Unknown Source) at org.gel.air.util.IOUtils.copyFile(Unknown Source) at org.gel.mauve.contigs.ContigOrderer.copyInputFiles(Unknown Source) at org.gel.mauve.contigs.ContigMauveAlignFrame.alignButtonActionPerformed(Unknown Source) at org.gel.mauve.gui.AlignFrame$9.actionPerformed(Unknown Source) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Running alignment. Executing win64\progressiveMauve --output=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1 --skip-refinement --weight=200 --output-guide-tree=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1.guide_tree --backbone-output=C:\Users\p270270\Desktop\CompGenTutorial\MauveOutput\alignment1\alignment1.backbone C:\Users\p270270\Desktop\CompGenTutorial\NC_011748.fna\NC_011748.fna C:\Users\p270270\Desktop\CompGenTutorial\SRR292770_unordered.fasta\SRR292770_unordered.fasta Exception FileNotOpened thrown from Unknown() in ..\libGenome\gnFileSource.cpp 67 Called by Unknown() Exited with error code: -1073741676 -- Maryam Chaib De Mares M.Sc. Evolutionary Biology PhD Candidate - Microbial Ecology Department Groningen Institute for Evolutionary Life Sciences (GELIFES) Rijksuniversiteit Groningen Nijenborgh 7, 9747 AG Groningen Linnaeusborg, room 0766 +31 50 363 2169 m.c...@ru... |
From: ZACHARY C. <zc...@wi...> - 2016-10-04 18:54:52
|
Hello Aaron, Thank you for your thorough reply. I do have access to UW's CHTC network. So, if I run progressivemauve distantly on Condor can I then visualize the outputs locally? Thanks again for this program. I'm attempting to align a de novo (Spades) assembly of an insect with its sister species and compare the outputs with a BWA using the same data. Go Badgers, Zach PS If academia doesn't work out there's always comedy! ________________________________ From: Aaron Darling <aar...@ut...> Sent: Tuesday, October 4, 2016 4:47:51 AM To: Rose Mark USRE; ZACHARY COHEN; mau...@li... Subject: Re: [Mauve-users] Crap. It's broke. Hi Zachary, Mark, et al, Glad you are able to see some humor in these error messages! Zachary, thanks for sending the log file. From that it looks like you are attempting an alignment of genomes that are 1.1Gbp and 597Mbp, respectively. It also appears that your computer has about 32GB of RAM, which unfortunately is not enough to build the sorted seed index datastructures in memory. So progressiveMauve is trying instead to build the index on disk, and there appears to be a bug in that very infrequently used functionality. If possible, I suggest getting a machine with a bit more RAM to do your genome alignment. As a rough guess 64GB may be enough, but I can't say with certainty. If that's not readily available in your department it's also possible to rent machines with large memory in the Amazon EC2 cloud, for a price of course. Best, -Aaron On Mon, 2016-10-03 at 17:11 +0000, Rose Mark USRE wrote: Don't have an answer but, damn, I respect the candidness of that error! From: ZACHARY COHEN [mailto:zc...@wi...] Sent: Sunday, October 02, 2016 11:12 PM To: mau...@li... Subject: [Mauve-users] Crap. It's broke. hello, I am trying to use Mauve to align my scaffolds.fa output from a Spades de novo assembly against a reference, but received an error. I've attached the error output file for your consideration and would greatly appreciate any feedback. Thanks again and I hope to hear from you soon. ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Mauve-users mailing list Mau...@li...<mailto:Mau...@li...> https://lists.sourceforge.net/lists/listinfo/mauve-users -- 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...> - 2016-10-04 13:57:13
|
Hi Rosie, apologies for the late reply, I am catching up on email and think the answer may be useful for others even if you have moved on from this work. First, the --scratch-path options control use of temporary storage when building sorted seed lists (sslist index files) for very large genomes where a single genome's index will not fit into RAM. In your case it will not have an effect because S. aureus genomes are fairly small. I would suggest running without those options and if it still exits with signal 11 (segmentation fault), it is possible that you need a machine with more RAM. The total amount of disk space required should not be more than a 10-20 GB for 100 genomes of the size of S. aureus. That said, progressiveMauve's compute time grows at least cubically in the sequence count, so you may find that it is too slow to align more than 50 or so genomes at once. Best, -Aaron On Fri, 2016-08-05 at 09:18 +1000, Rosemarie Sadsad wrote: > Dear users, > > I am trying to use progressiveMauve on 96 samples of S. aureus. I am > running this via command line on the university HPC and have > specified alternative scratch paths to allow more temporary storage > space. It stores (Storing raw sequence at ..) and loads (Sequence > loaded successfully..) only a subset of the samples and I receive the > error: > > Caught signal 11 > Cleaning up and exiting! > > Does anyone have any ideas on how to overcome this? > > Thank you for your help. > > Rosie > ------------------------------------------------------------------- > ----------- > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- 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...> - 2016-10-04 13:40:21
|
Hi Michael, I realize this is coming late, but still want to post a reply for the benefit of others who may be curious in the future. There are a number of ways to generate phylogenies from genome alignments. If you want to use Mauve I suggest doing the alignment with progressiveMauve then extracting the core genome alignment blocks with stripSubsetLCBs. From that point you could use ClonalFrameML or another alternative. There are some example instructions for these steps (and beyond that) on this page: https://github.com/xavierdidelot/ClonalOrigin/wiki/Usage On Fri, 2016-08-19 at 08:27 +0000, mic...@ag... wrote: > I am looking for a way to generate a phylogenetic tree of 30 > pseudomonas strains by using mauve. Since the guidetree outputted by > progressiveMauve is not a "real" phylogenetic tree I am looking for > another "whole genome approach". > > Would it be an option to generate a phylogenetic tree the following > way?: > 1. Get FastA file form 30 strains and concatenate into one file > 2. Align them with command: mauveAligner --output=ps.mauve.phylip -- > output-alignment=ps.alignment.phylip --weight=300 --alignment-output- > format=phylip --alignment-output-dir=. ../ inp/all/all.fasta > 3. Use raxml or fastree on the phylip which gets generated by > mauveAligner > > Thx > Michael > > ------------------------------------------------------------------- > ----------- > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- 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...> - 2016-10-04 13:31:05
|
Hi Cristina, apologies for the late reply, I am trying to get through the email backlog. Would you be able to send me the alignment, input sequences, and .backbone and .bbcols files off-list via google drive or something similar? It is not obvious to me why you would be getting an empty file so I would like to try to reproduce the problem on your data and then step through the code with a debugger. Best, -Aaron On Tue, 2016-09-20 at 16:13 -0300, Cristina Kraemer Zimpel wrote: > Hi, I am not using the command line (not sure if it run from the > command as well). > The version is MAUVE 2.4.0. > > the message in the MAUVE console: > after the alignment > "done. > root alignment has 84 superintervals > root alignment length: 4924424 > Organisms have 65.6% GC > Completed without error. > Alignment complete! > set 20, 2016 4:18:13 PM java.util.prefs.WindowsPreferences <init> > WARNING: Could not open/create prefs root node > Software\JavaSoft\Prefs at root 0x80000002. Windows > RegCreateKeyEx(...) returned error code 5." > > > > 2016-09-20 14:42 GMT-03:00 Joseph Fass <jos...@gm...>: > > Are you running the export from the GUI? (I'm not sure if there's a > > way to run it from the command line) > > Does it give you an error message in the GUI? > > What build / version of Mauve are you using? > > > > ~Joe > > > > 2016-09-20 7:19 GMT-07:00 Cristina Kraemer Zimpel > > l.com>: > > > > > > Hi > > > > > > I performed the progressive alignment with 7 Mycobacterial > > > genomes, and now I am trying to export gaps, unfortunately when I > > > choose this option I have as result an empty file. > > > Can anyone guide me here? > > > Thank you > > > -- > > > Cristina Kraemer Zimpel > > > > > > Médica Veterinária, Especialista em Medicina Veterinária do > > > Coletivo > > > Mestranda do Departamento de Medicina Veterinária Preventiva e > > > Saúde Animal (VPS) > > > Universidade de São Paulo - Faculdade de Medicina Veterinária e > > > Zootecnia > > > Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária > > > São Paulo, SP, CEP 05508 270, Brasil > > > > > > > > > --------------------------------------------------------------- > > > --------------- > > > > > > _______________________________________________ > > > Mauve-users mailing list > > > Mau...@li... > > > https://lists.sourceforge.net/lists/listinfo/mauve-users > > > > > > > > > -- > > Joseph Fass > > Bioinformatics Data Analyst > > UC Davis Genome Center - Bioinformatics Core > > http://bioinformatics.ucdavis.edu/ > > jn...@uc... > > phone ~ 530.752.2698 > > > > > -- > Cristina Kraemer Zimpel > > Médica Veterinária, Especialista em Medicina Veterinária do Coletivo > Mestranda do Departamento de Medicina Veterinária Preventiva e Saúde > Animal (VPS) > Universidade de São Paulo - Faculdade de Medicina Veterinária e > Zootecnia > Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária > São Paulo, SP, CEP 05508 270, Brasil > > ------------------------------------------------------------------- > ----------- > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- 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...> - 2016-10-04 10:04:06
|
Hi Zachary, Mark, et al, Glad you are able to see some humor in these error messages! Zachary, thanks for sending the log file. From that it looks like you are attempting an alignment of genomes that are 1.1Gbp and 597Mbp, respectively. It also appears that your computer has about 32GB of RAM, which unfortunately is not enough to build the sorted seed index datastructures in memory. So progressiveMauve is trying instead to build the index on disk, and there appears to be a bug in that very infrequently used functionality. If possible, I suggest getting a machine with a bit more RAM to do your genome alignment. As a rough guess 64GB may be enough, but I can't say with certainty. If that's not readily available in your department it's also possible to rent machines with large memory in the Amazon EC2 cloud, for a price of course. Best, -Aaron On Mon, 2016-10-03 at 17:11 +0000, Rose Mark USRE wrote: > Don’t have an answer but, damn, I respect the candidness of that > error! > > From: ZACHARY COHEN [mailto:zc...@wi...] > Sent: Sunday, October 02, 2016 11:12 PM > To: mau...@li... > Subject: [Mauve-users] Crap. It's broke. > > hello, > > I am trying to use Mauve to align my scaffolds.fa output from a > Spades de novo assembly against a reference, but received an error. > I've attached the error output file for your consideration and would > greatly appreciate any feedback. Thanks again and I hope to hear from > you soon. > > > This message may contain confidential information. If you are not the > designated recipient, please notify the sender immediately, and > delete the original and any copies. Any use of the message by you is > prohibited. > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- 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: Peter H. <pet...@ok...> - 2016-10-03 22:46:10
|
Sounds like the "/skeethocky mushrooms"/ problem again. peter On 10/02/2016 10:12 PM, ZACHARY COHEN wrote: > hello, > > I am trying to use Mauve to align my scaffolds.fa output from a Spades > de novo assembly against a reference, but received an error. I've > attached the error output file for your consideration and would > greatly appreciate any feedback. Thanks again and I hope to hear from > you soon. > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Rose M. U. <mar...@sy...> - 2016-10-03 17:11:48
|
Don't have an answer but, damn, I respect the candidness of that error! From: ZACHARY COHEN [mailto:zc...@wi...] Sent: Sunday, October 02, 2016 11:12 PM To: mau...@li... Subject: [Mauve-users] Crap. It's broke. hello, I am trying to use Mauve to align my scaffolds.fa output from a Spades de novo assembly against a reference, but received an error. I've attached the error output file for your consideration and would greatly appreciate any feedback. Thanks again and I hope to hear from you soon. ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. |
From: ZACHARY C. <zc...@wi...> - 2016-10-03 03:12:34
|
trying path ./linux-x64/progressiveMauve Running alignment. Executing ./linux-x64/progressiveMauve --output=/home/molecularecology/Desktop/mauveSPadesREf --output-guide-tree=/home/molecularecology/Desktop/mauveSPadesREf.guide_tree --backbone-output=/home/molecularecology/Desktop/mauveSPadesREf.backbone /home/molecularecology/Desktop/zcpb/refo/Ldec.genome.10062013.fa /home/molecularecology/Desktop/zcpb/spades_outputs/scaffolds.fasta Storing raw sequence at /tmp/rawseq21575.000 Sequence loaded successfully. /home/molecularecology/Desktop/zcpb/refo/Ldec.genome.10062013.fa 1170241964 base pairs. Storing raw sequence at /tmp/rawseq21575.001 Sequence loaded successfully. /home/molecularecology/Desktop/zcpb/spades_outputs/scaffolds.fasta 597642283 base pairs. Using weight 21 mers for initial seeds Creating sorted mer list Create time was: 154 seconds. Creating sorted mer list Create time was: 82 seconds. 0%..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%..100%.. done. using default bp penalty: 208036 using default bp estimate min score: 624107 Starting with 6987946 multi-matches Computing genome content distance matrix... Genome conservation distance matrix: 0 0.7505 0.7505 0 Writing guide tree to /home/molecularecology/Desktop/mauveSPadesREf.guide_tree reading tree... initializing alignment tree... Constructing seed occurrence lists for repeat detection Calculating pairwise breakpoint distances Pair 0, 1 has 4841563 initial LCBs Using scaled bp penalty: 4000 Pair (0,1) has 189698 well-supported breakpoints genome content distance matrix: 0 0.7505 0.7505 0 bp distance matrix: 0.9 0.9 0.9 0.9 Aligning... Aligning node 1 to 2 via 0! get ancestral matches Performing Sum-of-pairs Greedy Breakpoint Elimination construct LCB tracking matches There are 6381046 tracking matches There are 12762092 / 19143138 components used init tracking match LCB tracking pairwise score tracking matches get pairwise LCBs there are 4842018 pairwise LCBs scaling bp penalty by conservation weight: 0.7505 scaling bp penalty by bp weight: 0.9 Greedy BPE Scoring with scaled breakpoint penalty: 4000 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%..done Arrived at 188889 intervals Adding unaligned intervals addUnalignedIntervals yields 566486 intervals Merging unaligned intervals Marbling gaps Propagating descendant breakpoints descendant 0(1) has 1 intervals descendant 1(2) has 1 intervals propagateDescendantBreakpoints yields 188889 intervals Creating ancestral ordering Previous anchoring score: -1.79769e+308, new anchor score: 6.48718e+09 Backing up alignment tree... propagating ancestral breakpoints recursive anchor search Creating dmSML for seqI 0 Wrote raw sequence for seqI 0 Loaded sequence 0363140026b.p. MemTotal: 32840720 kB Crap. It's broke, return value 1 terminate called after throwing an instance of 'genome::gnException' Exited with error code: 134 |
From: Cristina K. Z. <cri...@gm...> - 2016-09-20 19:13:56
|
Hi, I am not using the command line (not sure if it run from the command as well). The version is MAUVE 2.4.0. the message in the MAUVE console: after the alignment "done. root alignment has 84 superintervals root alignment length: 4924424 Organisms have 65.6% GC Completed without error. Alignment complete! set 20, 2016 4:18:13 PM java.util.prefs.WindowsPreferences <init> WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5." 2016-09-20 14:42 GMT-03:00 Joseph Fass <jos...@gm...>: > Are you running the export from the GUI? (I'm not sure if there's a way to > run it from the command line) > Does it give you an error message in the GUI? > What build / version of Mauve are you using? > > ~Joe > > 2016-09-20 7:19 GMT-07:00 Cristina Kraemer Zimpel <cri...@gm...>: > >> >> Hi >> >> I performed the progressive alignment with 7 Mycobacterial genomes, and >> now I am trying to export gaps, unfortunately when I choose this option I >> have as result an empty file. >> Can anyone guide me here? >> Thank you >> -- >> Cristina Kraemer Zimpel >> >> Médica Veterinária, Especialista em Medicina Veterinária do Coletivo >> Mestranda do Departamento de Medicina Veterinária Preventiva e Saúde >> Animal (VPS) >> Universidade de São Paulo - Faculdade de Medicina Veterinária e Zootecnia >> Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária >> São Paulo, SP, CEP 05508 270, Brasil >> >> >> ------------------------------------------------------------ >> ------------------ >> >> _______________________________________________ >> Mauve-users mailing list >> Mau...@li... >> https://lists.sourceforge.net/lists/listinfo/mauve-users >> >> > > > -- > Joseph Fass > Bioinformatics Data Analyst > UC Davis Genome Center - Bioinformatics Core > http://bioinformatics.ucdavis.edu/ > jn...@uc... > phone ~ 530.752.2698 > -- Cristina Kraemer Zimpel Médica Veterinária, Especialista em Medicina Veterinária do Coletivo Mestranda do Departamento de Medicina Veterinária Preventiva e Saúde Animal (VPS) Universidade de São Paulo - Faculdade de Medicina Veterinária e Zootecnia Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária São Paulo, SP, CEP 05508 270, Brasil |
From: Joseph F. <jos...@gm...> - 2016-09-20 17:42:55
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Are you running the export from the GUI? (I'm not sure if there's a way to run it from the command line) Does it give you an error message in the GUI? What build / version of Mauve are you using? ~Joe 2016-09-20 7:19 GMT-07:00 Cristina Kraemer Zimpel <cri...@gm...>: > > Hi > > I performed the progressive alignment with 7 Mycobacterial genomes, and > now I am trying to export gaps, unfortunately when I choose this option I > have as result an empty file. > Can anyone guide me here? > Thank you > -- > Cristina Kraemer Zimpel > > Médica Veterinária, Especialista em Medicina Veterinária do Coletivo > Mestranda do Departamento de Medicina Veterinária Preventiva e Saúde > Animal (VPS) > Universidade de São Paulo - Faculdade de Medicina Veterinária e Zootecnia > Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária > São Paulo, SP, CEP 05508 270, Brasil > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > > -- Joseph Fass Bioinformatics Data Analyst UC Davis Genome Center - Bioinformatics Core http://bioinformatics.ucdavis.edu/ jn...@uc... phone ~ 530.752.2698 |
From: Cristina K. Z. <cri...@gm...> - 2016-09-20 14:19:12
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Hi I performed the progressive alignment with 7 Mycobacterial genomes, and now I am trying to export gaps, unfortunately when I choose this option I have as result an empty file. Can anyone guide me here? Thank you -- Cristina Kraemer Zimpel Médica Veterinária, Especialista em Medicina Veterinária do Coletivo Mestranda do Departamento de Medicina Veterinária Preventiva e Saúde Animal (VPS) Universidade de São Paulo - Faculdade de Medicina Veterinária e Zootecnia Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária São Paulo, SP, CEP 05508 270, Brasil |
From: <mic...@ag...> - 2016-08-19 08:39:45
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I am looking for a way to generate a phylogenetic tree of 30 pseudomonas strains by using mauve. Since the guidetree outputted by progressiveMauve is not a "real" phylogenetic tree I am looking for another "whole genome approach". Would it be an option to generate a phylogenetic tree the following way?: 1. Get FastA file form 30 strains and concatenate into one file 2. Align them with command: mauveAligner --output=ps.mauve.phylip --output-alignment=ps.alignment.phylip --weight=300 --alignment-output-format=phylip --alignment-output-dir=. ../ inp/all/all.fasta 3. Use raxml or fastree on the phylip which gets generated by mauveAligner Thx Michael |
From: Walter, M. <ma...@wa...> - 2016-08-18 16:52:02
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Hi Cristina, to help you further, it would be helpful, if you provide the error message you got as well as the type of input files you are using. And indeed, you can use prokaryotic contigs. I'm regularly align contigs in multiple fasta files (one fasta file per organism) against fasta or genbank of a reference genome. Most of the time it works straightforward. Sometimes I have to remove dashes (-) from the fasta header lines, if present. -- Kind regards, Mathias Am 18.08.2016 6:15 nachm. schrieb "Cristina Kraemer Zimpel" < ck...@gm...>: > Hello > I wonder if can I perform progressive alignment with MAUVE using contigs > of prokaryotic genomes? > I have tried but the analysis just stops, so I think I am using the > contigs as input file incorrectly. > Can you give some light here? > Thank you so much for your time > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > > |
From: Cristina K. Z. <ck...@gm...> - 2016-08-18 15:26:29
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Hello I wonder if can I perform progressive alignment with MAUVE using contigs of prokaryotic genomes? I have tried but the analysis just stops, so I think I am using the contigs as input file incorrectly. Can you give some light here? Thank you so much for your time |
From: Walter, M. <ma...@wa...> - 2016-08-17 12:21:24
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Hi Cristina, sorry, I better had answered to the Mauve mailing list. Indeed, you can perform the alignment with many drafts and as long as you just want to extract the SNPs afterwards, it does not matter, if the contigs are ordered or not. But just in case you will look for genome rearrangements or if some SNPs are located in a coding region, I recommend ordering the contigs before. I also recommend ordering just one draft genome using the GUI and than running the remaining reorderings at the command line in a loop. You can just copy the corresponding command from the log window and adapt it. -- Regards, Mathias 2016-08-17 13:26 GMT+02:00 Cristina Kraemer Zimpel <cri...@gm...>: > Hi Mathias, thank you for the tips. > If you allow me, I would like to ask another question. > Can I perform multiple alignment with many drafts? Or should I reorder the > contigs one at time with the reference and look for gap closure to perform > the multiple alignment? > > > Thank you again > > > 2016-08-17 2:22 GMT-03:00 Walter, Mathias <ma...@wa...>: > >> Hi Cristina, >> >> >> reordering of the contigs is always a good idea. Additionally, I usually >> rotate it to move the oriC to the start of the linearized chromosome. That >> makes visual inspection much easier. The contig mover produces 1 to n >> folders named alignment1 to alignmentN and put the reordered contigs into a >> fasta file having the same name as you original file. For tracing the >> reorder process, you can look at the tab file. >> >> Be carefull with reference-based SNP coordinates. Sometimes they are >> increases by one in the middle of the genome. I used ParSNP ( >> https://github.com/marbl/parsnp) to circumvent this. It can read the >> XMFA files produced by Mauve. >> >> -- >> Regards, >> Mathias >> >> 2016-08-17 1:16 GMT+02:00 Cristina Kraemer Zimpel <cri...@gm...> >> : >> >>> Greetings >>> I intend to align genomes of Mycobacterium strains in order to find SNPs >>> using MAUVE. Few genomes are complete and few are draft. >>> >>> For the draft genomes. Should I reorder the contigs with the reference:? >>> And which output file after reorder contigs should I use for the >>> comparison with complete genomes. >>> Thank you >>> Best regards. >>> >>> -- >>> Cristina Kraemer Zimpel >>> >>> Médica Veterinária, Especialista em Medicina Veterinária do Coletivo >>> Mestranda em Epidemiologia Experimental Aplicada às Zoonoses >>> >>> Departamento de Medicina Veterinária Preventiva e Saúde Animal (VPS), >>> FMVZ - USP >>> Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária >>> São Paulo, SP, CEP 05508 270, Brasil >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> >>> _______________________________________________ >>> Mauve-users mailing list >>> Mau...@li... >>> https://lists.sourceforge.net/lists/listinfo/mauve-users >>> >>> >> > > > -- > Cristina Kraemer Zimpel > > Médica Veterinária, Especialista em Medicina Veterinária do Coletivo > Mestranda em Epidemiologia Experimental Aplicada às Zoonoses > > Departamento de Medicina Veterinária Preventiva e Saúde Animal (VPS), FMVZ > - USP > Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária > São Paulo, SP, CEP 05508 270, Brasil > > |
From: Cristina K. Z. <cri...@gm...> - 2016-08-16 23:16:44
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Greetings I intend to align genomes of Mycobacterium strains in order to find SNPs using MAUVE. Few genomes are complete and few are draft. For the draft genomes. Should I reorder the contigs with the reference:? And which output file after reorder contigs should I use for the comparison with complete genomes. Thank you Best regards. -- Cristina Kraemer Zimpel Médica Veterinária, Especialista em Medicina Veterinária do Coletivo Mestranda em Epidemiologia Experimental Aplicada às Zoonoses Departamento de Medicina Veterinária Preventiva e Saúde Animal (VPS), FMVZ - USP Av. Prof. Dr. Orlando Marques de Paiva, 87 - Cidade Universitária São Paulo, SP, CEP 05508 270, Brasil |
From: mali s. <ma...@ar...> - 2016-08-15 06:50:03
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Dear users I try to reorder assembled contigs (de novo assembly of 500Mb plant genome. I have ~1M scaffolds) based on reference genome. I used the command nohup java -Xmx100G -cp /home/mauve_2.3.1/Mauve.jar org.gel.mauve.contigs.ContigOrderer -output ./ -ref /data/genomes/vitis/ref.fa -draft ../scafSeq & The program finish running without errors, but except of the alignment1 directory, no output files were created. The last lines in the log file, and the content of alignment1 directory are below Any idea what got wrong? Thanks Mali Greedy BPE Scoring with scaled breakpoint penalty: 4000 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%..done Arrived at 180991 intervals Adding unaligned intervals addUnalignedIntervals yields 540256 intervals Merging unaligned intervals Marbling gaps Propagating descendant breakpoints descendant 0(1) has 1 intervals descendant 1(2) has 1 intervals propagateDescendantBreakpoints yields 180991 intervals Creating ancestral ordering Previous anchoring score: -1.79769e+308, new anchor score: 9.25996e+09 Backing up alignment tree... propagating ancestral breakpoints recursive anchor search The alignment1 directory contains the following files: 472M ref.fa 640M scafSeq 2.0G ref.fa.sslist 2.6G scafSeq.sslist 0 alignment1 (empty) 31 alignment1.guide_tree -- ================================ Mali Salmon-Divon, PhD Department of Molecular Biology Ariel University Ariel, ISRAEL Phone: +972-546-350197 <ma...@ar...> Email: ma...@ar... |
From: Rosemarie S. <r.s...@un...> - 2016-08-04 23:18:48
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Dear users, I am trying to use progressiveMauve on 96 samples of S. aureus. I am running this via command line on the university HPC and have specified alternative scratch paths to allow more temporary storage space. It stores (Storing raw sequence at ..) and loads (Sequence loaded successfully..) only a subset of the samples and I receive the error: Caught signal 11 Cleaning up and exiting! Does anyone have any ideas on how to overcome this? Thank you for your help. Rosie |