mauve-users — A general discussion forum for users of mauve-related software

Re: [Mauve-users] Guide tree question

[Amarin C. <ama...@gm...>]

Aaron,

Could the guide tree be used to group samples within a serotype or would
that too be a misinterpretation?

-Amarin

On Tue, Dec 8, 2015 at 4:41 PM, Aaron Darling <aar...@ut...>
wrote:

> Hi Susan,
>
> On Tue, 2015-12-08 at 20:05 +0000, Susan Beth Fogelson wrote:
>
> Thank you for all of your helpful responses.  I guess at this point my
> question changes.  I would like to build a phylogenetic tree of this
> alignment and I assume I need to convert the XMFA file to another format to
> complete this task.  Has anyone had experience with file conversion and
> what program would you recommend for phylogenetic tree reconstruction?  At
> present I am using MEGA6 but I think these files are too big for that
> program to run effectively.
>
>
> There are many ways to build phylogenies from Mauve alignments and
> hopefully others on the list will chime in with suggestions. Once you have
> an initial tree, you might consider ClonalFrameML as a way to help reduce
> the impact of historical recombination events on tree inference:
> https://github.com/xavierdidelot/clonalframeml/wiki
>
> 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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Re: [Mauve-users] new user

[Aaron D. <aar...@ut...>]

Hi Enrico, it looks like you may have run the software from the command
line on a machine without an X11 display. Can you confirm?
The java component of Mauve is primarily for visualizing genome
alignments and usually requires a display. If you want to calculate an
genome alignment from the command line I will refer you to the
progressiveMauve tool, which was bundled in your Mauve download:
http://darlinglab.org/mauve/user-guide/progressivemauve.html

Best,
-Aaron

On Tue, 2016-01-12 at 18:29 +0100, Enrico Tortoli wrote:
> Dear all
> 
>  
> 
> I have downloaded MAUVE and installed it on my PC with Linux (Ubuntu
> 64 bits). Please find attached the report I get when attempting to run
> the software.  
> 
> Is it a problem of Java? Others programs requiring Java don’t seem to
> have problems.
> 
> Thanks for your help
> 
> 
> 
>  
> 
> e
> 
>  
> 
> 
> 
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-- 
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia

http://darlinglab.org
twitter: @koadman




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[Mauve-users] stripSubsetLCBs error

[Prabh B. <bas...@gm...>]

Hello Users, 

I have used progressive mauve to align 42 genomes and then used the stripSubsetLCBs to extract the core genome. However, now when I try to open my core alignment using the Mauve GUI it gives me an error. 

Exception in thread "Thread-4" java.lang.ArrayIndexOutOfBoundsException: genome E.fergusonii_ATCC.fasta position 1
    at org.gel.mauve.XMFAAlignment.getLCB(Unknown Source)
    at org.gel.mauve.XMFAAlignment.getRange(Unknown Source)
    at org.gel.mauve.SimilarityIndex.calculateIndex(Unknown Source)
    at org.gel.mauve.SimilarityIndex.<init>(Unknown Source)
    at org.gel.mauve.XmfaViewerModel.init(Unknown Source)
    at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source)
    at org.gel.mauve.ModelBuilder.buildModel(Unknown Source)
    at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source)
    at org.gel.mauve.gui.FrameLoader.run(Unknown Source)
    at java.lang.Thread.run(Thread.java:745)

Any ideas on what the error is and how I can fix it. 

Thanks for you time
Prabh

[Mauve-users] new user

[Enrico T. <e.t...@li...>]

aar...@ut...

Exception in thread "AWT-EventQueue-0" java.awt.HeadlessException
	at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
	at java.awt.Window.<init>(Window.java:535)
	at java.awt.Frame.<init>(Frame.java:420)
	at java.awt.Frame.<init>(Frame.java:385)
	at javax.swing.JFrame.<init>(JFrame.java:174)
	at gr.zeus.ui.JConsole.<init>(JConsole.java:84)
	at gr.zeus.ui.JConsole.getConsole(JConsole.java:121)
	at org.gel.mauve.MyConsole.setUseSwing(Unknown Source)
	at org.gel.mauve.gui.Mauve.init(Unknown Source)
	at org.gel.mauve.gui.Mauve$2.run(Unknown Source)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:745)
	at java.awt.EventQueue.access$300(EventQueue.java:103)
	at java.awt.EventQueue$3.run(EventQueue.java:706)
	at java.awt.EventQueue$3.run(EventQueue.java:704)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:77)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:715)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

Re: [Mauve-users] xmfa2fasta.pl question

[Aaron D. <aar...@ut...>]

Hi Susan,
I am guessing you refer to the xmfa2fasta.pl script posted to this list
by Lu Cheng some years ago? If so, it is still available via the
attachments link on this mailing list archive page:
http://sourceforge.net/p/mauve/mailman/mauve-users/thread/51F...@he.../

a little googling also turns up a newer script of the same name, but
different implementation:
https://github.com/kjolley/seq_scripts/blob/master/xmfa2fasta.pl

Best,
-Aaron


On Mon, 2015-12-21 at 20:39 +0000, Susan Beth Fogelson wrote:
> Hi,
> 
>  
> 
> I am trying to extract my LCBs from an alignment of 33 bacterial
> genomes to construct a core alignment.  I am looking for a working
> link to the xmfa2fasta.pl. Does anyone have this file that they can
> share?  Thanks
> 
>  
> 
> -Susan
> 
>  
> 
> Susan Fogelson, DVM, MS, Dipl. ACVP
> 
> Aquatic Animal Anatomic Pathologist and PhD candidate
> 
> fo...@ug...
> 
> 706-542-5859
> 
>  
> 
> 
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> 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




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Re: [Mauve-users] Mauve problem - unknown sequences

[Aaron D. <aar...@ut...>]

Hi Nina, 

I suggest reading Guy Plunkett's reply in an earlier discussion on this
topic and writing back if you have further questions:
http://sourceforge.net/p/mauve/mailman/message/31561527/

Best,
-Aaron


On Fri, 2015-12-18 at 10:25 +0100, Nina Schleimer wrote:
> Hello,
> 
> I got a problem using progressiveMauve alignment fuction.
> If I use fasta files everything works fine. 
> Cause I need the annotations I tried to add genbank files. 
> There are no error messages (see below) in the console and everything 
> looks good, except that there are no sequence names. The three 
> different sequences I used are called "unknown" so that I can not 
> distinguish between the three sequences.
> 
> Mauve console: 
> done.
> root alignment has 2 superintervals
> root alignment length: 2800653
> Organisms have 32.9% GC
> Completed without error.
> Alignment complete!
> 
> 
> Thanks for your help,
> 
> Nina 
> 
> ------------------------------------------------------------------------------
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> 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




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[Mauve-users] xmfa2fasta.pl question

[Susan B. F. <fo...@ug...>]

Hi,

I am trying to extract my LCBs from an alignment of 33 bacterial genomes to construct a core alignment.  I am looking for a working link to the xmfa2fasta.pl. Does anyone have this file that they can share?  Thanks

-Susan

Susan Fogelson, DVM, MS, Dipl. ACVP
Aquatic Animal Anatomic Pathologist and PhD candidate
fo...@ug...<mailto:fo...@ug...>
706-542-5859

[Mauve-users] Mauve problem - unknown sequences

[Nina S. <nin...@we...>]

Hello,

I got a problem using progressiveMauve alignment fuction.
If I use fasta files everything works fine.
Cause I need the annotations I tried to add genbank files.
There are no error messages (see below) in the console and everything
looks good, except that there are *no sequence names*. The three
different sequences I used are called "unknown" so that I can not
distinguish between the three sequences.


Mauve console:
done.
root alignment has 2 superintervals
root alignment length: 2800653
Organisms have 32.9% GC
Completed without error.
Alignment complete!


Thanks for your help,

Nina

Re: [Mauve-users] "LCB weight"-scale

[Aaron D. <aar...@ut...>]

Hi Anna,

On Wed, 2015-12-16 at 11:04 +0100, Anna Schuster wrote:

> Hi there,
> 
> I´m using the Mauve software and I have a short question. I´ve been
> desperately searching the web for an answer but I can´t find it:
> 
> I did a multiple alignment of 7 sequences and I´d be interested in
> answering the following questions:
> - how many locally collinear blocks (LCBs) were built in my alignment?


In 2-way genome alignments there is a straightforward answer to this
question, one simply counts the number of breakpoints. However for n-way
genome alignments with n > 2 this quantity is not well-defined due to
the existence of hidden breakpoints. You can read more about the issue
in this publication by Kehr et al:
http://arxiv.org/abs/1207.6964
When calculating the alignment, progressiveMauve uses pairwise LCBs to
build up the multiple genome alignment.



> - mean length of LCBs?


see above. this quantity could only be calculated for pairwise
projections, or on strictly core genome material (as in the original
mauveAligner or via application of stripSubsetLCBs to a progressiveMauve
alignment).


> - shortest/longest block?


same issues.


> - multiple alignment of the 'core' region on average covered ...% ?


This is a quantity you should be able to obtain with some simple
processing of the .backbone file with your favorite program. Excel,
LibreOffice, R, Python should all be able to easily parse the
tab-delimited text file.


> - nucleotide diversity (Π) for the concatenated aligned region
> was ...?


Mauve doesn't come with automated tools to calculate a quantity like
this, but it would certainly be possible to cook something up with some
basic scripting.
 


> 
> 1. To answer those questions it´ll be important to see the "LCB
> weight"-scale in the viewer. I downloaded a file from an online
> publication (attachment 1), where they have that scale (upper corner
> right). But I don´t find a way to show this feature in my own
> alignment. Can you help me with that?


Yes, that LCB weight slider will appear in pairwise alignments where the
concept is well defined.


> 
> 2. and where can I find the nucleotide diversity?
> 


see above. likely to require some scripting, at the very least to
concatenate alignment blocks into a single multi-fasta alignment for
subsequent processing with another existing tool to calculate the
quantity (assuming such a tool exists for standard multi-fasta
alignments).


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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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.
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Re: [Mauve-users] Exporting ordered contigs

[Walter, M. <ma...@wa...>]

Hi Rajeh,

you do not need to export them. Just look into the fasta files generated in
the output directory. They contain the ordered contigs. Ordering
information is stored in the xxx_contigs.tab file.

--
Regards,
Mathias

2015-12-16 19:05 GMT+01:00 Ahmad Rajeh <ra...@sl...>:

> Hello,
>
> Is it possible to export the contigs in the order they mapped to the
> reference after using Contigs Mover?
>
> Thanks,
> Rajeh
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Mauve-users mailing list
> Mau...@li...
> https://lists.sourceforge.net/lists/listinfo/mauve-users
>
>

[Mauve-users] Exporting ordered contigs

[Ahmad R. <ra...@sl...>]

Hello,

Is it possible to export the contigs in the order they mapped to the
reference after using Contigs Mover?

Thanks,
Rajeh

[Mauve-users] "LCB weight"-scale

[Anna S. <ann...@tu...>]

Hi there,

I´m using the Mauve software and I have a short question. I´ve been 
desperately searching the web for an answer but I can´t find it:

I did a multiple alignment of 7 sequences and I´d be interested in 
answering the following questions:
- how many locally collinear blocks (LCBs) were built in my alignment?
- mean length of LCBs?
- shortest/longest block?
- multiple alignment of the 'core' region on average covered ...% ?
- nucleotide diversity (Π) for the concatenated aligned region was ...?

1. To answer those questions it´ll be important to see the "LCB 
weight"-scale in the viewer. I downloaded a file from an online 
publication (attachment 1), where they have that scale (upper corner 
right). But I don´t find a way to show this feature in my own alignment. 
Can you help me with that?

2. and where can I find the nucleotide diversity?

Thanks for your help and the nice software! Anna

-- 
Dipl.Biol. Anna-Kathrin Schuster
Wissenschaftliche Mitarbeiterin

Technische Universität Berlin
Fakultät III/Technischer Umweltschutz
FG Umweltmikrobiologie

Ernst-Reuter-Platz 1
10587 Berlin
030-31473752

Re: [Mauve-users] Guide tree question

[Aaron D. <aar...@ut...>]

Hi Susan,

On Tue, 2015-12-08 at 20:05 +0000, Susan Beth Fogelson wrote:
> Thank you for all of your helpful responses.  I guess at this point my
> question changes.  I would like to build a phylogenetic tree of this
> alignment and I assume I need to convert the XMFA file to another
> format to complete this task.  Has anyone had experience with file
> conversion and what program would you recommend for phylogenetic tree
> reconstruction?  At present I am using MEGA6 but I think these files
> are too big for that program to run effectively.


There are many ways to build phylogenies from Mauve alignments and
hopefully others on the list will chime in with suggestions. Once you
have an initial tree, you might consider ClonalFrameML as a way to help
reduce the impact of historical recombination events on tree inference:
https://github.com/xavierdidelot/clonalframeml/wiki

Best,
-Aaron
-- 
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.

Re: [Mauve-users] Guide tree question

[Susan B. F. <fo...@ug...>]

Thank you for all of your helpful responses.  I guess at this point my question changes.  I would like to build a phylogenetic tree of this alignment and I assume I need to convert the XMFA file to another format to complete this task.  Has anyone had experience with file conversion and what program would you recommend for phylogenetic tree reconstruction?  At present I am using MEGA6 but I think these files are too big for that program to run effectively.

Thanks,

Susan

From: Aaron Darling [mailto:da...@cs...]
Sent: Tuesday, December 08, 2015 2:32 PM
To: mau...@li...
Subject: Re: [Mauve-users] Guide tree question

The vagueness in that file is at least partially intentional -- the tree doesn't have a well-established interpretation outside of being a reflection of the order in which genomes were aligned. I think it would be dangerous to interpret it as a phylogeny, especially as one intended to represent vertical inheritance, as the topology is shaped heavily by gene content and there are well documented cases where independent lineages have converged in gene content (e.g. Shigella) and I've seen the guide tree and phylogeny conflict strongly in such datasets.

Best,
-Aaron

On Tue, 2015-12-08 at 14:09 -0500, Amarin Cogburn wrote:
As far as I know there is no way to have the file/sample names appended to the guide tree.  The sequence order is the order in which the files were added in the alignment setup.  I've been manually changing the seq names in the guide tree file.  If there is another way of doing it I'd love to hear it as it does get cumbersome when you have more than a handful of sequences.

On Tue, Dec 8, 2015 at 12:29 PM, Susan Beth Fogelson <fo...@ug...<mailto:fo...@ug...>> wrote:


Hello,



I used progressive mauve to align 32 genomes, which produced a guide tree file.  When I opened this file in Geneious the labels on the tree are not my original sequence labels. The new labels just say seq 1, seq 2, seq 3, etc  up to seq 32.  I was wondering if there is a way to visualize my original sequence labels on this tree?



-Susan

Susan Fogelson, DVM, MS, Dipl. ACVP

Aquatic Animal Anatomic Pathologist and PhD candidate

fo...@ug...<mailto:fo...@ug...>

706-542-5859<tel:706-542-5859>




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Re: [Mauve-users] Guide tree question

[Aaron D. <da...@cs...>]

The vagueness in that file is at least partially intentional -- the tree
doesn't have a well-established interpretation outside of being a
reflection of the order in which genomes were aligned. I think it would
be dangerous to interpret it as a phylogeny, especially as one intended
to represent vertical inheritance, as the topology is shaped heavily by
gene content and there are well documented cases where independent
lineages have converged in gene content (e.g. Shigella) and I've seen
the guide tree and phylogeny conflict strongly in such datasets.

Best,
-Aaron

On Tue, 2015-12-08 at 14:09 -0500, Amarin Cogburn wrote:
> As far as I know there is no way to have the file/sample names
> appended to the guide tree.  The sequence order is the order in which
> the files were added in the alignment setup.  I've been manually
> changing the seq names in the guide tree file.  If there is another
> way of doing it I'd love to hear it as it does get cumbersome when you
> have more than a handful of sequences. 
> 
> 
> On Tue, Dec 8, 2015 at 12:29 PM, Susan Beth Fogelson <fo...@ug...>
> wrote:
> 
>          
>         
>         Hello,
>         
>          
>         
>         I used progressive mauve to align 32 genomes, which produced a
>         guide tree file.  When I opened this file in Geneious the
>         labels on the tree are not my original sequence labels. The
>         new labels just say seq 1, seq 2, seq 3, etc  up to seq 32.  I
>         was wondering if there is a way to visualize my original
>         sequence labels on this tree?
>         
>          
>         
>         -Susan 
>         
>         Susan Fogelson, DVM, MS, Dipl. ACVP
>         
>         Aquatic Animal Anatomic Pathologist and PhD candidate
>         
>         fo...@ug...
>         
>         706-542-5859
>         
>          
>         
>         
>         
>         
>         ------------------------------------------------------------------------------
>         Go from Idea to Many App Stores Faster with Intel(R) XDK
>         Give your users amazing mobile app experiences with Intel(R)
>         XDK.
>         Use one codebase in this all-in-one HTML5 development
>         environment.
>         Design, debug & build mobile apps & 2D/3D high-impact games
>         for multiple OSs.
>         http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>         _______________________________________________
>         Mauve-users mailing list
>         Mau...@li...
>         https://lists.sourceforge.net/lists/listinfo/mauve-users
>         
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> Mauve-users mailing list
> Mau...@li...
> https://lists.sourceforge.net/lists/listinfo/mauve-users

Re: [Mauve-users] Guide tree question

[Amarin C. <ama...@gm...>]

As far as I know there is no way to have the file/sample names appended to
the guide tree.  The sequence order is the order in which the files were
added in the alignment setup.  I've been manually changing the seq names in
the guide tree file.  If there is another way of doing it I'd love to hear
it as it does get cumbersome when you have more than a handful of
sequences.

On Tue, Dec 8, 2015 at 12:29 PM, Susan Beth Fogelson <fo...@ug...>
wrote:

>
>
> Hello,
>
>
>
> I used progressive mauve to align 32 genomes, which produced a guide tree
> file.  When I opened this file in Geneious the labels on the tree are not
> my original sequence labels. The new labels just say seq 1, seq 2, seq 3,
> etc  up to seq 32.  I was wondering if there is a way to visualize my
> original sequence labels on this tree?
>
>
>
> -Susan
>
> Susan Fogelson, DVM, MS, Dipl. ACVP
>
> Aquatic Animal Anatomic Pathologist and PhD candidate
>
> fo...@ug...
>
> 706-542-5859
>
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
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> Mau...@li...
> https://lists.sourceforge.net/lists/listinfo/mauve-users
>
>

[Mauve-users] Guide tree question

[Susan B. F. <fo...@ug...>]

Hello,

I used progressive mauve to align 32 genomes, which produced a guide tree file.  When I opened this file in Geneious the labels on the tree are not my original sequence labels. The new labels just say seq 1, seq 2, seq 3, etc  up to seq 32.  I was wondering if there is a way to visualize my original sequence labels on this tree?

-Susan
Susan Fogelson, DVM, MS, Dipl. ACVP
Aquatic Animal Anatomic Pathologist and PhD candidate
fo...@ug...<mailto:fo...@ug...>
706-542-5859

Re: [Mauve-users] Help with aligning fungal genomes with pMauve

[Taruna A. <ta...@wi...>]

Hello. I just wanted to follow up on my email below. Thoughts from anyone? Thanks for your help in advance! 

Taruna

> On Nov 26, 2015, at 7:47 AM, Taruna Aggarwal <ta...@wi...> wrote:
> 
>  I have a de novo assembly of a fungus and I’m trying to generate synteny maps for it. I would like to use pMauve aligner to accomplish this goal but I have some questions regarding the program and the results I’ve been getting. 
> 
> Initially I ran pMauve aligner with all default parameters to get a sense of the program. Next, I changed a few parameters and got the alignment results that do not show large syntenic blocks for a self to self alignment (Grosmannia_clavigera_genome to Grosmanni_clavigera_genome). Additionally, I expected more syntenic regions between my two genomes of interest (gm5_allpaths_scaffolds aligned to Grosmannia_clavigera) than the results show. I have been changing the LCB weight around and when I choose a small value, there are several LCB connecting lines. I understand what LCBs are but I don’t understand what changing the LCB weight does to the alignment. Lastly, if anyone has any suggestions as to which parameters I should change, I would really appreciate them. Thank you very much for your help! I have attached screenshots of the alignments in question and the parameters I used. Please let me know if I can clarify anything. Thanks again!
> 
> Taruna
> 
> <Screen Shot 2015-11-25 at 10.40.54 AM.png>
> <Screen Shot 2015-11-25 at 4.46.01 PM.png><Screen Shot 2015-11-25 at 4.45.45 PM.png>
> 

Re: [Mauve-users] progressiveMauve exited with error code 137

[Becca L. <Rac...@nd...>]

Thanks, Aaron.

To follow up in case someone else has a similar error and comes looking for
the answer, I moved the alignment to a node with more memory and it ran
without a problem. I can't absolutely rule out /tmp but it was probably the
memory.

On Thu, Nov 26, 2015 at 6:44 PM, Aaron Darling <aar...@ut...>
wrote:

> Hi Becca, thanks for writing about this and for sending the console
> output. It helps.
>
> Exit code 137 is fairly generic, indicating the progressiveMauve process
> was killed with signal 9, which is something that can either be done
> manually or by the system I think. Insight here:
> http://tldp.org/LDP/abs/html/exitcodes.html
>
> Yes, progressiveMauve uses /tmp. If /tmp is limited you might try pointing
> the software to store temporary files in another location by setting $TMP
> or $TMPDIR .  Apparently this hasn't been working for everybody so I'd
> suggest testing on a small dataset first to confirm that the rawseq* and
> guide tree etc temporary files land in the specified directory before
> launching a long-running alignment.
>
> It could also be a memory usage issue... you might wrap the call to
> progressiveMauve with /usr/bin/time -v to get a record of the peak memory
> allocation. linuxes will kill processes that consume too much RAM, though
> different kernel versions behave differently in this regard.
>
> Best,
> -Aaron
>
>
>
> On Wed, 2015-11-25 at 15:20 -0500, Becca Love wrote:
>
> Hi all,
>
>
> I'm trying to align three closely-related invertebrate genomes of about
> 275 Mbp using progressiveMauve (console output pasted below). I have
> previously aligned similar genomes, but this time I'm getting an error code
> of 137, which I haven't seen described elsewhere. I have 70G RAM and should
> have sufficient hard drive space, though there could possibly be a conflict
> with large backups being temporarily written to /tmp overnight.
>
>
> So my questions are:
>
>
> 1.) does error code 137 signify a disk space shortage, and if not,
>
> 2.) can you give me any other information on this code?
>
>
> Thanks,
>
> Becca
>
>
> ##console output:
>
> trying path ./linux-x64/progressiveMauve
>
> Running alignment.
>
> Executing
>
> progressiveMauve
>
>     --output=taxon1-taxon2-outgroup
>
>     --output-guide-tree=taxon1-taxon2-outgroup.guide_tree
>
>     --backbone-output=taxon1-taxon2-outgroup.backbone
>
>     /media/labcomp/NGSdata/taxon1.fa
>
>     /media/labcomp/NGSdata/taxon2.fa
>
>     /media/labcomp/NGSdata/outgroup.fa
>
> Storing raw sequence at /tmp/rawseq12032.000
>
> Sequence loaded successfully.
>
> /media/labcomp/NGSdata/taxon1.fa 273109044 base pairs.
>
> Storing raw sequence at /tmp/rawseq12032.001
>
> Sequence loaded successfully.
>
> /media/labcomp/NGSdata/taxon2.fa 273109044 base pairs.
>
> Storing raw sequence at /tmp/rawseq12032.002
>
> Sequence loaded successfully.
>
> /media/labcomp/NGSdata/outgroup.fa 283828998 base pairs.
>
> Using weight 19 mers for initial seeds
>
> Creating sorted mer list
>
> Create time was: 48 seconds.
>
> Creating sorted mer list
>
> Create time was: 48 seconds.
>
> Creating sorted mer list
>
> Create time was: 44 seconds.
>
> 0%..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%..done.
>
> using default bp penalty: 196306
>
> using default bp estimate min score: 588917
>
> Starting with 9524545 multi-matches
>
> Computing genome content distance matrix...
>
>
>
> Genome conservation distance matrix:
>
> 0    0.104825    0.439205
>
> 0.104825    0    0.441706
>
> 0.439205    0.441706    0
>
>
> Writing guide tree to taxon1-taxon2-outgroup.guide_tree
>
> reading tree...
>
> initializing alignment tree...
>
> Constructing seed occurrence lists for repeat detection
>
> Calculating pairwise breakpoint distances
>
> Pair 0, 1 has 327147 initial LCBs
>
> Using scaled bp penalty: 378169
>
> Pair (0,1) has 1 well-supported breakpoints
>
> Pair 0, 2 has 1022274 initial LCBs
>
> Using scaled bp penalty: 58246.4
>
> Pair (0,2) has 1791 well-supported breakpoints
>
> Pair 1, 2 has 1042887 initial LCBs
>
> Using scaled bp penalty: 57214.3
>
> Pair (1,2) has 1817 well-supported breakpoints
>
> genome content distance matrix:
>
> 0    0.104825    0.439205
>
> 0.104825    0    0.441706
>
> 0.439205    0.441706    0
>
>
> bp distance matrix:
>
> 0.9    0.000216867    0.38841
>
> 0.000216867    0.9    0.394048
>
> 0.38841    0.394048    0.9
>
>
> Aligning...
>
> Aligning node 3 to 4 via 1!
>
> get ancestral matches
>
> Performing Sum-of-pairs Greedy Breakpoint Elimination
>
> construct LCB tracking matches
>
> There are 2488444 tracking matches
>
> There are 4976888 / 12442220 components used
>
> init tracking match LCB tracking
>
> pairwise score tracking matches
>
> get pairwise LCBs
>
> there are 327509 pairwise LCBs
>
> scaling bp penalty by conservation weight:
>
> 0.104825
>
>
>
> scaling bp penalty by bp weight:
>
> 0.000216867
>
>
> Greedy BPE
>
> Scoring with scaled breakpoint penalty: 126002
>
> 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%..done
>
> Arrived at 1 intervals
>
> Adding unaligned intervals
>
> addUnalignedIntervals yields 3 intervals
>
> Merging unaligned intervals
>
> Marbling gaps
>
> Propagating descendant breakpoints
>
> descendant 0(3) has 1 intervals
>
> descendant 1(4) has 1 intervals
>
> propagateDescendantBreakpoints yields 1 intervals
>
> Creating ancestral ordering
>
> Previous anchoring score: -1.79769e+308, new anchor score: 1.26132e+10
>
> Backing up alignment tree...
>
> propagating ancestral breakpoints
>
> recursive anchor search
>
> 0,0 have 2 new matches outside LCBs
>
> 0,0 has an additional 17332 matches
>
> Restoring backed up alignment tree...
>
> 1,0 has 17332 pairwise matches
>
> Performing Sum-of-pairs Greedy Breakpoint Elimination
>
> construct LCB tracking matches
>
> There are 2202926 tracking matches
>
> There are 4405852 / 11014630 components used
>
> init tracking match LCB tracking
>
> pairwise score tracking matches
>
> get pairwise LCBs
>
> there are 348 pairwise LCBs
>
> scaling bp penalty by conservation weight:
>
> 0.104825
>
>
>
> scaling bp penalty by bp weight:
>
> 0.000216867
>
>
> Greedy BPE
>
> Scoring with scaled breakpoint penalty: 126002
>
> 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%..done
>
> Arrived at 3 intervals
>
> Adding unaligned intervals
>
> addUnalignedIntervals yields 11 intervals
>
> Merging unaligned intervals
>
> Marbling gaps
>
> Propagating descendant breakpoints
>
> descendant 0(3) has 1 intervals
>
> descendant 1(4) has 1 intervals
>
> propagateDescendantBreakpoints yields 3 intervals
>
> Creating ancestral ordering
>
> Previous anchoring score: 1.26132e+10, new anchor score: 1.12416e+10
>
> propagating ancestral breakpoints
>
> performing a gapped alignment
>
>
> 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%..
>
> 100%..Fix left ends
>
>
> done.
>
> Aligning node 1 to 2 via 0!
>
> get ancestral matches
>
> Performing Sum-of-pairs Greedy Breakpoint Elimination
>
> construct LCB tracking matches
>
> There are 3284810 tracking matches
>
> There are 13008197 / 16424050 components used
>
> init tracking match LCB tracking
>
> pairwise score tracking matches
>
> get pairwise LCBs
>
> there are 2179961 pairwise LCBs
>
> scaling bp penalty by conservation weight:
>
> 0.439205
>
> 0.441706
>
>
>
> scaling bp penalty by bp weight:
>
> 0.38841
>
> 0.394048
>
>
> Greedy BPE
>
> Scoring with scaled breakpoint penalty: 7262.22
>
> 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%..done
>
> Arrived at 10742 intervals
>
> Adding unaligned intervals
>
> addUnalignedIntervals yields 32131 intervals
>
> Merging unaligned intervals
>
> Marbling gaps
>
> Propagating descendant breakpoints
>
> descendant 0(1) has 1 intervals
>
> descendant 1(2) has 1 intervals
>
> propagateDescendantBreakpoints yields 10742 intervals
>
> Creating ancestral ordering
>
> Previous anchoring score: -1.79769e+308, new anchor score: 1.6137e+10
>
> Backing up alignment tree...
>
> propagating ancestral breakpoints
>
> Exited with error code: 137
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> 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.
>
>
>
> ------------------------------------------------------------------------------
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> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
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>
>

Re: [Mauve-users] progressive mauve stop working with any error

[Aaron D. <aar...@ut...>]

Hi Prabh,

by default, top sorts processes in descending order of CPU usage. If
progressiveMauve has exhausted all available memory, it may not be using
any CPU but instead simply waiting for data to be swapped between main
memory & disk storage, in which case it may not show up in top. If you
run something like:
ps -aux 
(or ps -ef on the mac) 
it should give a full process list which is a more definitive answer on
whether something is running or not, and what it may be doing.

If you see it there, and the memory usage is near or beyond the total
amount of RAM installed in your system, then it is likely that the
aligner has simply run out of memory and is unlikely to finish any time
soon. However, it might be possible to run it on a machine with more
RAM. If it has died entirely without error (on either stdout or stderr)
then we will need to investigate your dataset further.

-Aaron


On Fri, 2015-11-27 at 09:29 -0500, Prabh Basra wrote:

> Hi All, 
> 
> 
> 
> I am using progressive mauve to align 42 bacterial genomes (E. coli ),
> Mauve was running for about 8 days and then it stopped without giving
> any error. I am attaching the console output. There is no error,
> however it has been stuck at this point for a day and when I check if
> its running using “top”, its not running. 
> 
> 
> Any suggestion about what is going on. 
> 
> 
> Thanks 
> 
> Prabh Basra
> MSc Candidate, Carleton University
> bas...@gm...
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> 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.

[Mauve-users] progressive mauve stop working with any error

[Prabh B. <bas...@gm...>]

Hi All, 

I am using progressive mauve to align 42 bacterial genomes (E. coli ), Mauve was running for about 8 days and then it stopped without giving any error. I am attaching the console output. There is no error, however it has been stuck at this point for a day and when I check if its running using “top”, its not running. 

Any suggestion about what is going on. 

Thanks 
Prabh Basra
MSc Candidate, Carleton University
bas...@gm...

Re: [Mauve-users] progressiveMauve exited with error code 137

[Aaron D. <aar...@ut...>]

Hi Becca, thanks for writing about this and for sending the console
output. It helps.

Exit code 137 is fairly generic, indicating the progressiveMauve process
was killed with signal 9, which is something that can either be done
manually or by the system I think. Insight here:
http://tldp.org/LDP/abs/html/exitcodes.html

Yes, progressiveMauve uses /tmp. If /tmp is limited you might try
pointing the software to store temporary files in another location by
setting $TMP or $TMPDIR .  Apparently this hasn't been working for
everybody so I'd suggest testing on a small dataset first to confirm
that the rawseq* and guide tree etc temporary files land in the
specified directory before launching a long-running alignment.

It could also be a memory usage issue... you might wrap the call to
progressiveMauve with /usr/bin/time -v to get a record of the peak
memory allocation. linuxes will kill processes that consume too much
RAM, though different kernel versions behave differently in this regard.

Best,
-Aaron


On Wed, 2015-11-25 at 15:20 -0500, Becca Love wrote:
> Hi all,
> 
> 
> I'm trying to align three closely-related invertebrate genomes of
> about 275 Mbp using progressiveMauve (console output pasted below). I
> have previously aligned similar genomes, but this time I'm getting an
> error code of 137, which I haven't seen described elsewhere. I have
> 70G RAM and should have sufficient hard drive space, though there
> could possibly be a conflict with large backups being temporarily
> written to /tmp overnight.
> 
> 
> So my questions are:
> 
> 
> 1.) does error code 137 signify a disk space shortage, and if not,
> 
> 2.) can you give me any other information on this code?
> 
> 
> Thanks,
> 
> Becca
> 
> 
> ##console output:
> 
> trying path ./linux-x64/progressiveMauve
> 
> Running alignment.
> 
> Executing
> 
> progressiveMauve
> 
>     --output=taxon1-taxon2-outgroup
> 
>     --output-guide-tree=taxon1-taxon2-outgroup.guide_tree
> 
>     --backbone-output=taxon1-taxon2-outgroup.backbone
> 
>     /media/labcomp/NGSdata/taxon1.fa
> 
>     /media/labcomp/NGSdata/taxon2.fa
> 
>     /media/labcomp/NGSdata/outgroup.fa
> 
> Storing raw sequence at /tmp/rawseq12032.000
> 
> Sequence loaded successfully.
> 
> /media/labcomp/NGSdata/taxon1.fa 273109044 base pairs.
> 
> Storing raw sequence at /tmp/rawseq12032.001
> 
> Sequence loaded successfully.
> 
> /media/labcomp/NGSdata/taxon2.fa 273109044 base pairs.
> 
> Storing raw sequence at /tmp/rawseq12032.002
> 
> Sequence loaded successfully.
> 
> /media/labcomp/NGSdata/outgroup.fa 283828998 base pairs.
> 
> Using weight 19 mers for initial seeds
> 
> Creating sorted mer list
> 
> Create time was: 48 seconds.
> 
> Creating sorted mer list
> 
> Create time was: 48 seconds.
> 
> Creating sorted mer list
> 
> Create time was: 44 seconds.
> 
> 0%..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%..done.
> 
> using default bp penalty: 196306
> 
> using default bp estimate min score: 588917
> 
> Starting with 9524545 multi-matches
> 
> Computing genome content distance matrix...
> 
> 
> 
> Genome conservation distance matrix:
> 
> 0    0.104825    0.439205
> 
> 0.104825    0    0.441706
> 
> 0.439205    0.441706    0
> 
> 
> Writing guide tree to taxon1-taxon2-outgroup.guide_tree
> 
> reading tree...
> 
> initializing alignment tree...
> 
> Constructing seed occurrence lists for repeat detection
> 
> Calculating pairwise breakpoint distances
> 
> Pair 0, 1 has 327147 initial LCBs
> 
> Using scaled bp penalty: 378169
> 
> Pair (0,1) has 1 well-supported breakpoints
> 
> Pair 0, 2 has 1022274 initial LCBs
> 
> Using scaled bp penalty: 58246.4
> 
> Pair (0,2) has 1791 well-supported breakpoints
> 
> Pair 1, 2 has 1042887 initial LCBs
> 
> Using scaled bp penalty: 57214.3
> 
> Pair (1,2) has 1817 well-supported breakpoints
> 
> genome content distance matrix:
> 
> 0    0.104825    0.439205
> 
> 0.104825    0    0.441706
> 
> 0.439205    0.441706    0
> 
> 
> bp distance matrix:
> 
> 0.9    0.000216867    0.38841
> 
> 0.000216867    0.9    0.394048
> 
> 0.38841    0.394048    0.9
> 
> 
> Aligning...
> 
> Aligning node 3 to 4 via 1!
> 
> get ancestral matches
> 
> Performing Sum-of-pairs Greedy Breakpoint Elimination
> 
> construct LCB tracking matches
> 
> There are 2488444 tracking matches
> 
> There are 4976888 / 12442220 components used
> 
> init tracking match LCB tracking
> 
> pairwise score tracking matches
> 
> get pairwise LCBs
> 
> there are 327509 pairwise LCBs
> 
> scaling bp penalty by conservation weight:
> 
> 0.104825
> 
> 
> 
> scaling bp penalty by bp weight:
> 
> 0.000216867
> 
> 
> Greedy BPE
> 
> Scoring with scaled breakpoint penalty: 126002
> 
> 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%..done
> 
> Arrived at 1 intervals
> 
> Adding unaligned intervals
> 
> addUnalignedIntervals yields 3 intervals
> 
> Merging unaligned intervals
> 
> Marbling gaps
> 
> Propagating descendant breakpoints
> 
> descendant 0(3) has 1 intervals
> 
> descendant 1(4) has 1 intervals
> 
> propagateDescendantBreakpoints yields 1 intervals
> 
> Creating ancestral ordering
> 
> Previous anchoring score: -1.79769e+308, new anchor score: 1.26132e+10
> 
> Backing up alignment tree...
> 
> propagating ancestral breakpoints
> 
> recursive anchor search
> 
> 0,0 have 2 new matches outside LCBs
> 
> 0,0 has an additional 17332 matches
> 
> Restoring backed up alignment tree...
> 
> 1,0 has 17332 pairwise matches
> 
> Performing Sum-of-pairs Greedy Breakpoint Elimination
> 
> construct LCB tracking matches
> 
> There are 2202926 tracking matches
> 
> There are 4405852 / 11014630 components used
> 
> init tracking match LCB tracking
> 
> pairwise score tracking matches
> 
> get pairwise LCBs
> 
> there are 348 pairwise LCBs
> 
> scaling bp penalty by conservation weight:
> 
> 0.104825
> 
> 
> 
> scaling bp penalty by bp weight:
> 
> 0.000216867
> 
> 
> Greedy BPE
> 
> Scoring with scaled breakpoint penalty: 126002
> 
> 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%..done
> 
> Arrived at 3 intervals
> 
> Adding unaligned intervals
> 
> addUnalignedIntervals yields 11 intervals
> 
> Merging unaligned intervals
> 
> Marbling gaps
> 
> Propagating descendant breakpoints
> 
> descendant 0(3) has 1 intervals
> 
> descendant 1(4) has 1 intervals
> 
> propagateDescendantBreakpoints yields 3 intervals
> 
> Creating ancestral ordering
> 
> Previous anchoring score: 1.26132e+10, new anchor score: 1.12416e+10
> 
> propagating ancestral breakpoints
> 
> performing a gapped alignment
> 
> 
> 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%..
> 
> 100%..Fix left ends
> 
> 
> done.
> 
> Aligning node 1 to 2 via 0!
> 
> get ancestral matches
> 
> Performing Sum-of-pairs Greedy Breakpoint Elimination
> 
> construct LCB tracking matches
> 
> There are 3284810 tracking matches
> 
> There are 13008197 / 16424050 components used
> 
> init tracking match LCB tracking
> 
> pairwise score tracking matches
> 
> get pairwise LCBs
> 
> there are 2179961 pairwise LCBs
> 
> scaling bp penalty by conservation weight:
> 
> 0.439205
> 
> 0.441706
> 
> 
> 
> scaling bp penalty by bp weight:
> 
> 0.38841
> 
> 0.394048
> 
> 
> Greedy BPE
> 
> Scoring with scaled breakpoint penalty: 7262.22
> 
> 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%..done
> 
> Arrived at 10742 intervals
> 
> Adding unaligned intervals
> 
> addUnalignedIntervals yields 32131 intervals
> 
> Merging unaligned intervals
> 
> Marbling gaps
> 
> Propagating descendant breakpoints
> 
> descendant 0(1) has 1 intervals
> 
> descendant 1(2) has 1 intervals
> 
> propagateDescendantBreakpoints yields 10742 intervals
> 
> Creating ancestral ordering
> 
> Previous anchoring score: -1.79769e+308, new anchor score: 1.6137e+10
> 
> Backing up alignment tree...
> 
> propagating ancestral breakpoints
> 
> Exited with error code: 137
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> 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
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[Mauve-users] Help with aligning fungal genomes with pMauve

[Taruna A. <ta...@wi...>]

 I have a de novo assembly of a fungus and I’m trying to generate synteny maps for it. I would like to use pMauve aligner to accomplish this goal but I have some questions regarding the program and the results I’ve been getting. 

Initially I ran pMauve aligner with all default parameters to get a sense of the program. Next, I changed a few parameters and got the alignment results that do not show large syntenic blocks for a self to self alignment (Grosmannia_clavigera_genome to Grosmanni_clavigera_genome). Additionally, I expected more syntenic regions between my two genomes of interest (gm5_allpaths_scaffolds aligned to Grosmannia_clavigera) than the results show. I have been changing the LCB weight around and when I choose a small value, there are several LCB connecting lines. I understand what LCBs are but I don’t understand what changing the LCB weight does to the alignment. Lastly, if anyone has any suggestions as to which parameters I should change, I would really appreciate them. Thank you very much for your help! I have attached screenshots of the alignments in question and the parameters I used. Please let me know if I can clarify anything. Thanks again!

Taruna

[Mauve-users] progressiveMauve exited with error code 137

[Becca L. <Rac...@nd...>]

Hi all,

I'm trying to align three closely-related invertebrate genomes of about 275
Mbp using progressiveMauve (console output pasted below). I have previously
aligned similar genomes, but this time I'm getting an error code of 137,
which I haven't seen described elsewhere. I have 70G RAM and should have
sufficient hard drive space, though there could possibly be a conflict with
large backups being temporarily written to /tmp overnight.

So my questions are:

1.) does error code 137 signify a disk space shortage, and if not,

2.) can you give me any other information on this code?

Thanks,

Becca

##console output:

trying path ./linux-x64/progressiveMauve

Running alignment.

Executing

progressiveMauve

    --output=taxon1-taxon2-outgroup

    --output-guide-tree=taxon1-taxon2-outgroup.guide_tree

    --backbone-output=taxon1-taxon2-outgroup.backbone

    /media/labcomp/NGSdata/taxon1.fa

    /media/labcomp/NGSdata/taxon2.fa

    /media/labcomp/NGSdata/outgroup.fa

Storing raw sequence at /tmp/rawseq12032.000

Sequence loaded successfully.

/media/labcomp/NGSdata/taxon1.fa 273109044 base pairs.

Storing raw sequence at /tmp/rawseq12032.001

Sequence loaded successfully.

/media/labcomp/NGSdata/taxon2.fa 273109044 base pairs.

Storing raw sequence at /tmp/rawseq12032.002

Sequence loaded successfully.

/media/labcomp/NGSdata/outgroup.fa 283828998 base pairs.

Using weight 19 mers for initial seeds

Creating sorted mer list

Create time was: 48 seconds.

Creating sorted mer list

Create time was: 48 seconds.

Creating sorted mer list

Create time was: 44 seconds.

0%..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%..done.

using default bp penalty: 196306

using default bp estimate min score: 588917

Starting with 9524545 multi-matches

Computing genome content distance matrix...


Genome conservation distance matrix:

0    0.104825    0.439205

0.104825    0    0.441706

0.439205    0.441706    0

Writing guide tree to taxon1-taxon2-outgroup.guide_tree

reading tree...

initializing alignment tree...

Constructing seed occurrence lists for repeat detection

Calculating pairwise breakpoint distances

Pair 0, 1 has 327147 initial LCBs

Using scaled bp penalty: 378169

Pair (0,1) has 1 well-supported breakpoints

Pair 0, 2 has 1022274 initial LCBs

Using scaled bp penalty: 58246.4

Pair (0,2) has 1791 well-supported breakpoints

Pair 1, 2 has 1042887 initial LCBs

Using scaled bp penalty: 57214.3

Pair (1,2) has 1817 well-supported breakpoints

genome content distance matrix:

0    0.104825    0.439205

0.104825    0    0.441706

0.439205    0.441706    0

bp distance matrix:

0.9    0.000216867    0.38841

0.000216867    0.9    0.394048

0.38841    0.394048    0.9

Aligning...

Aligning node 3 to 4 via 1!

get ancestral matches

Performing Sum-of-pairs Greedy Breakpoint Elimination

construct LCB tracking matches

There are 2488444 tracking matches

There are 4976888 / 12442220 components used

init tracking match LCB tracking

pairwise score tracking matches

get pairwise LCBs

there are 327509 pairwise LCBs

scaling bp penalty by conservation weight:

0.104825


scaling bp penalty by bp weight:

0.000216867

Greedy BPE

Scoring with scaled breakpoint penalty: 126002

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%..done

Arrived at 1 intervals

Adding unaligned intervals

addUnalignedIntervals yields 3 intervals

Merging unaligned intervals

Marbling gaps

Propagating descendant breakpoints

descendant 0(3) has 1 intervals

descendant 1(4) has 1 intervals

propagateDescendantBreakpoints yields 1 intervals

Creating ancestral ordering

Previous anchoring score: -1.79769e+308, new anchor score: 1.26132e+10

Backing up alignment tree...

propagating ancestral breakpoints

recursive anchor search

0,0 have 2 new matches outside LCBs

0,0 has an additional 17332 matches

Restoring backed up alignment tree...

1,0 has 17332 pairwise matches

Performing Sum-of-pairs Greedy Breakpoint Elimination

construct LCB tracking matches

There are 2202926 tracking matches

There are 4405852 / 11014630 components used

init tracking match LCB tracking

pairwise score tracking matches

get pairwise LCBs

there are 348 pairwise LCBs

scaling bp penalty by conservation weight:

0.104825


scaling bp penalty by bp weight:

0.000216867

Greedy BPE

Scoring with scaled breakpoint penalty: 126002

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%..done

Arrived at 3 intervals

Adding unaligned intervals

addUnalignedIntervals yields 11 intervals

Merging unaligned intervals

Marbling gaps

Propagating descendant breakpoints

descendant 0(3) has 1 intervals

descendant 1(4) has 1 intervals

propagateDescendantBreakpoints yields 3 intervals

Creating ancestral ordering

Previous anchoring score: 1.26132e+10, new anchor score: 1.12416e+10

propagating ancestral breakpoints

performing a gapped alignment

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%..

100%..Fix left ends

done.

Aligning node 1 to 2 via 0!

get ancestral matches

Performing Sum-of-pairs Greedy Breakpoint Elimination

construct LCB tracking matches

There are 3284810 tracking matches

There are 13008197 / 16424050 components used

init tracking match LCB tracking

pairwise score tracking matches

get pairwise LCBs

there are 2179961 pairwise LCBs

scaling bp penalty by conservation weight:

0.439205

0.441706


scaling bp penalty by bp weight:

0.38841

0.394048

Greedy BPE

Scoring with scaled breakpoint penalty: 7262.22

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%..done

Arrived at 10742 intervals

Adding unaligned intervals

addUnalignedIntervals yields 32131 intervals

Merging unaligned intervals

Marbling gaps

Propagating descendant breakpoints

descendant 0(1) has 1 intervals

descendant 1(2) has 1 intervals

propagateDescendantBreakpoints yields 10742 intervals

Creating ancestral ordering

Previous anchoring score: -1.79769e+308, new anchor score: 1.6137e+10

Backing up alignment tree...

propagating ancestral breakpoints

Exited with error code: 137

Re: [Mauve-users] Mauve Contigu Mover Code

[Aaron D. <aar...@ut...>]

Hi Rajeh,

The contig mover is in the org.gel.mauve.contigs package. Probably
ContigOrderer.java and ContigReorderer.java are the two places you might
start from.

Best,
-Aaron


On Mon, 2015-11-23 at 13:47 -0600, Ahmad Rajeh wrote:

> Hello,
> 
> I’d like to look into the contig mover code and see if I can expand on it. The problem is I can’t really find it. Could you please help me locating it? I have the entire Mauve package setup in eclipse.
> 
> Thanks,
> Rajeh
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> 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.