Hello Guy,
Thanks for pointing out this issue.
This sounds like a relatively trivial matter to fix. I have added a
sourceforge bug report which can be used to track progress on solving
the issue:
http://sourceforge.net/tracker/index.php?func=detailaid=1942680group_id=181544atid=897627
-Aaron
Hello Robert, some responses below...
Ingraham, Robert wrote:
I am trying run mauve using a Linux platform, it ‘hangs up” after
about 15 minutes. This is my fifth attempt, is there anything obvious
I am doing wrong?
I am using a FASTA multi file as input.
This is the command line file:
JASON J FLOWERS wrote:
I have been using Mauve in linux for quite a while with no problems, but
after not running an alignment for several months, my linux installation no
longer works, I can start up Mauve (2.1) and the initial screen opens
without issue. When I select File -align or
The 2.3.0 Mauve build was done on an Intel Mac running OS X 10.5.
Previous release builds (which worked on ppc) were done on Intel running
10.4.x. Although I no longer have a PowerPC machine available for
testing, I did test the PowerPC build using Apple's Rosetta ppc
emulation in 10.5 and it
Hi Daniel,
Please contact me off-list to resolve source code compilation errors --
I think they are probably not relevant to most people on this list.
In response to your other question: I have not recently built libGenome,
libMems, or mauveAligner with the proprietary intel compilers. Perhaps
Hi Evan,
On Wed, 2010-04-21 at 10:42 -0400, Snitkin, Evan (NIH/NHGRI) [F] wrote:
I was wondering if anyone knew of a way to have mauve output a snps and
ortholog output file from the command line, instead of having to use the gui.
There's no way to do that with the Mauve 2.3.1 release. It
Hi Anastasia:
On Mon, 2010-05-03 at 14:10 -0700, Anastasia Gioti wrote:
terminate called after throwing an instance of 'std::ios_base::failure'
what(): failed mapping file: Invalid argument
Exited with error code: 134
Although this error message may seem cryptic, you are almost
Hi Jason,
It's taken me a couple days to get to it, but I've written a little
program that can read XMFA and write out MAF. It's called xmfa2maf and
it will appear in the other programs links for your favorite OS on the
mauve snapshots site in the next day or so.
Beware, however, that even
Hi Evan,
On Wed, 2010-11-24 at 13:42 -0500, Snitkin, Evan (NIH/NHGRI) [F] wrote:
Hello,
I have an extremely mundane question. I am using the ortholog exporter and
would like some additional flexibility in the alignment coverage threshold.
Right now it is required that the coverage be
Hi Diego,
On Wed, 2013-07-10 at 16:43 +0200, dpa...@cipf.es wrote:
BUT I would need get a file with the position of the LCBs on each
genome, that is, the start and end position of each LCB refered to each
scaffold of each genome.
Actually, that information that I need, is shown in the
Hello Hiren, (reply below)
On Tue, 2013-07-09 at 16:59 +0200, Hiren Ghosh wrote:
Dear All, I used MIRA for genome assembly and i got contigfile
Ecoli-1_out.unpadded.fasta. Now i want to do alignment with this
contig with another Ecoli genome refseq.fasta. In command line i am
typinglike
Hello Hiren,
On Tue, 2013-07-16 at 20:23 +1000, Hiren Ghosh wrote:
Dear all,
I am using mauve contig mover through command line .I have a
question: once i am running mauve contig mover i am getting n number
iteration for each run and for each run mauve generate one folder name
alignment1,
Hi Jingjing,
Please try using one of the more recent snapshot releases of Mauve
available here:
http://gel.ahabs.wisc.edu/mauve/snapshots/
for example this build for linux:
http://gel.ahabs.wisc.edu/mauve/snapshots/2012/2012-06-07/linux-x64/mauve_linux_snapshot_2012-06-07.tar.gz
The dependency
Hi Zhao,
The aligner is not able to open the sequence files for one reason or
another, it's not clear why. You might try checking the access
permissions for those files directories, or simply downloading the
data aligner to a different computer (linux?) and running it there.
Best,
-Aaron
On
Hi Brianna,
It looks like you're using version 2.3.1 of Mauve to align some 2Gbp+
mouse genomes. There was an unfortunate bug in that release which
prevented the alignment of such large genomes. The snapshot releases
available here should have that fixed:
http://gel.ahabs.wisc.edu/mauve/snapshots
Hi Shlomo,
On Sun, 2013-09-15 at 20:39 +0200, Shlomo Blum wrote:
1. Should I reorder all the drafts against the same reference genome
from NCBI, or should I reorder the control strain first, and then
reorder the other strains against the reordered control strain
(after concatenating the
Hi Danny,
I believe this problem has been cropping up on Macs for several years.
The images are not damaged. The issue (I think) is that they are not
cryptographically signed with a key issued by Apple. If you temporarily
disable the zealous security settings, see here:
Hi Silvia,
The program appears to be terminating as its attempting to create a
temporary file to store a raw format version of your sequence. I
wonder if there are problems writing to the /var/folders/yk/...
directory, possibly due to permissions problems or a full disk. Disk
space and large file
Hi Cristell, hope this info isn't too late to be useful.
On Thu, 2013-10-24 at 07:48 +1100, Cristell Navarro wrote:
Hi all
I would like to know how could I generate the .islands file and what is
the information that the file .bbcols is showing...
The .islands file is only generated by
Hi Silvia,
After thinking about this for a while I am beginning to suspect there
may be a problem with the input files. Would it be possible for you to
send me the input files off-list either via compressed e-mail attachment
or dropbox so I can test it?
Thanks,
-Aaron
On Mon, 2013-10-14 at
Hi Gabriel,
On Fri, 2013-11-08 at 07:10 +1100, Gabriel Andres Gallina Nizzo wrote:
Hello. I'm running progressive mauve in 54 genomes of ~3mb. I have
BioLinux 7, CPU Athlon X6 and 8GB RAM. So far so good but it's running
for 72 hours and fin the last 24 hours it's at the same point
according
Hi Leonor,
Yes, it is possible to export a list of SNPs from the command-line if
you are using one of the snapshot releases available from here:
http://gel.ahabs.wisc.edu/mauve/snapshots
The command-line syntax to do so is:
java -cp Mauve.jar org.gel.mauve.analysis.SnpExporter -f aln.xmfa -o
Hi Laura,
Thanks for writing. Yes, you are correct that 0 in the .backbone file
indicates that a particular genome lacks a positional homolog for that
region. As for the coordinate system, the aligner concatenates all
contigs into a single coordinate system and does this in the same order
that
Hi Talia, the XMFA file includes filesystem path references to the
original aligned sequences. stripSubsetLCBs tries to read in those
sequences, but is unable to open the at least one of the files and that
is why it's throwing the FileNotOpened exception. If the sequence files
have moved you might
Hi Alejandro, can you provide more details about why you are unable to
carry out more than one genome alignment in Mauve when running on
Windows 7? Is there any error message in the log window?
Cheers,
-Aaron
On Sun, 2014-04-27 at 06:00 +1000, Alejandro Acosta González wrote:
Hi everyone,
I
Hi Mariam,
Perhaps the easiest way to do this is via the graphical interface. If
you load the final alignment generated by the contig mover in the Mauve
viewer, any unplaced contigs will appear on the right side of the draft
genome track. They will be unaligned, and therefore will not have any
Hi Eric,
what version of Mauve are you using?
All recent (e.g. in the past 5 years) builds have included 64-bit intel
support for Mac OS X. They work on OS X 10.7. There are powerpc versions
included in the 'fat' binaries. If you get the this snapshot:
Hi Lunwen,
It seems that your user account does not have write access to the
directory where the sequences are located. Try moving them into My
Documents or an equivalent directory in your user account.
Also, is there a reason you are not using progressiveMauve for
alignment? mauveAligner is only
Hi Ray,
As the error states, xmfa2maf does not support alignments that span
multiple contigs or chromosomes. This would be a nice feature to have
but isn't exactly trivial to implement. One workaround might be to
concatenate all of your sequences prior to alignment, although that may
complicate
Hello Kai,
On Thu, 2014-05-08 at 07:54 +1000, Zhou, K (mmb) wrote:
We recently wanna fish the unique sequences from a set of genomes. Is
there any script can do this task after alignment by Mauve?
There isn't any script to do this within the Mauve software
independently of annotations,
Hi Manal,
On Wed, 2014-05-28 at 23:45 +1000, Manal Farid wrote:
this is very useful but why when blast one of the unordered contigs it
shows 100% similarity to the reference (but it was not aligned
properly by Mauve.
this happens frequently when the contig has sequence for a multi-copy
gene
Hi Tina,
On Thu, 2014-06-05 at 00:42 -0400, Tina Lan wrote:
Hi,
It would be really great if anyone could give me some advice on how to
activate the mauve assembly metrics within Mauve GUI. Thanks a lot!
What version of Mauve have you downloaded? The assembly metrics are only
available in
Hello Hiren,
On Wed, 2014-06-04 at 15:02 +0200, Hiren Ghosh wrote:
Hello all i was trying to run mauve as a batch mode in such a way
for draft in *.fasta
do
echo $draft
#$ref= Ecoli_jj1886_complete_geneone.fasta;
$bname=echo $draft
java -Xmx500m -cp Mauve.jar
Hi Carmela, apologies for the delayed response.
Without seeing the exact details of what you're observing, e.g. with a
screenshot, it's hard for me to know whether this is actually a bug or
some confusion in the interpretation of how the viewer displays the
alignment. Just to clarify a bit: the
!
-Julie
On 13/07/2014 7:43 PM, Aaron Darling wrote:
Hi Julie,
There will be another release with a traditional numeric version
identifier eventually, but as it currently stands the development
snapshots are about as stable as research software gets. There are a
number of cosmetic bugs
Hi Jonas, this is an issue that's specific to the Java VM that you're
using. I just wrote a separate message about it but the short story
workaround is that if you can switch to the Sun VM the problem should go
away.
On Wed, 2014-06-25 at 00:57 +1000, Jonas Torgny Larsson wrote:
Dear all,
I
Hi Cristina,
Mauve uses a GenBank sequence file parser implemented in BioJava 1.7,
which is somewhat strict brittle in its interpretation of the format.
If you can provide the error messages that appear in the Mauve console
log when you load the alignment then myself or someone else on the list
Hi Bhav,
A handful of things changed in the implementation of library functions
during the development of progressiveMauve (the main new feature in the
2.x release series) that also changed mauveAligner (because they use
some of the same library functions). I don't have a summary of the
details of
Hi Tina, this appears to be a bug in the Mauve snapshot you are using.
Would you be able to provide me with a copy of the sequence files
alignment so I can track down the problem and fix it? In the meantime,
if you obtain the 2.3.1 release version from here:
Hi Manal,
The first two steps outlined on this page provide one example for how a
collection of genomes can be aligned and from them a phylogeny inferred:
http://code.google.com/p/clonalorigin/wiki/FromGenomeAssemblyToRecombination
Best,
-Aaron
On Tue, 2014-06-17 at 19:13 +1000, Manal Farid
Hi Saleh, I realize this reply is coming quite late. Hopefully it is
still useful. more below...
On Wed, 2014-06-18 at 09:43 +1000, Saleh T wrote:
I used progressivemauve to compare two genomes each saved in the fasta
file format. In each genome file there are more than one sequence
Hello Berthold,
On Mon, 2014-08-11 at 13:34 +0200, heinze wrote:
genes (as per the GenBank file annotation). However, the exported file
just lists the coordinates of the GenBank genome, without any sign of
comparing to the second, fasta sequence. This is regardless of which
features I select
Hi Julie,
I have success with the java 6u45 on ubuntu provided by the webupd8team
ppa.
Best,
-Aaron
On Thu, 2014-08-14 at 16:26 -0700, Julie Shay wrote:
Thanks for replying! I believe we are using Sun JDK. This is what's
returned when I enter the command java -version:
java version 1.7.0_06
Hi Stephanie,
In regard to your first question, it's not obvious why the alignment
would open the first time with annotations but would fail in subsequent
opens. Can you send a copy paste of any messages in the console log
window please? Another thing that might be worth trying would be to
clear
genome alignment on the ordered,
annotated contigs if you so wish.
Best,
-Aaron
From: Shlomo Blum [shlomo.b...@mail.huji.ac.il]
Sent: Thursday, September 11, 2014 3:55 AM
To: Aaron Darling
Cc: mauve-users@lists.sourceforge.net
Subject: Re: [Mauve-users
Hello Hannah,
On Sun, 2014-09-07 at 19:03 -0400, Hannah Fehlner-Peach wrote:
Why are the regions of dissimilarity at different points in the two
corresponding LCBs? This seems to contradict the idea that the two
genomes are aligned to each other. Any help is appreciated!
It's not clear
Hi Marco, apologies for the delay in replying.
It is possible to manually create a shortcut. To do so, you will need to
find the javaw.exe executable that comes with your Java installation.
Create a shortcut to javaw (you can do this from the right-click context
menu in windows 7, not sure about
previous
email. Exactly which version of a Java VM will make this work? Also,
please let me know if/when there is any development towards fixing
this problem. Thanks again!
-Julie
On 12/08/2014 11:00 AM, Aaron Darling wrote:
Hi Julie, apologies for the delayed response.
Matt
-Original Message-
From: Aaron Darling [mailto:aaron.darl...@uts.edu.au]
Sent: Tuesday, 11 November 2014 11:33 p.m.
To: mauve-users@lists.sourceforge.net
Subject: Re: [Mauve-users] alignment of 15 genomes with varying degrees of
similarity
Hello Anja,
On Tue, 2014-11-11 at 14:32
Dear Mauvonauts, some of you have been waiting very patiently (5 years!)
for a new Mauve release. Well, the wait is over. Mauve 2.4.0 has been
released with a number of important bugfixes, usability improvements,
and even a few new features.
I would also like to announce that the Mauve web site
Hi Cristina,
Recent versions of OS X (e.g. Yosemite) require Java apps such as Mauve
to be signed by the app developer with a cryptographic certificate
purchased from Apple. I have obtained such a certificate and used it to
sign a new Mauve release, v2.4.0, available here:
Hello Franz,
I was able to identify and resolved the bug in the 2.4.0 which led to
the scoring error on linux and crashes on some other platforms. The fix
is now in the source code repository and I've posted an updated snapshot
for linux:
Hi Swetha, it appears your system does not recognize mauveAligner as an
executable program. Can you please tell me exactly what operating system
and version (32 or 64-bit, kernel and glibc version) you are using?
Best,
-Aaron
On Thu, 2015-02-12 at 20:51 +1100, Swetha Gopal wrote:
I downloaded
Hello Franz, thanks for reporting this. You are not the only person
experiencing this issue with Mauve 2.4.0. It looks like a bug! I am
planning to take a close look and work on a fix just as soon as
Australian grant-writing deadlines pass in a couple weeks.
Best,
-Aaron
On Tue, 2015-02-10 at
Hi Michael, great to see some discussion on this topic.
I'll try to give some answers. The boundaries of the homologous segments
are defined by an HMM on a pairwise basis among all genomes. The process
is described in a few of the publications, e.g. Treangen et al 2009 and
Darling et al 2010.
Hi Cristina,
There seems to be a problem with the way the Mauve GUI tries to cache
some of the sequence data the first time the alignment is opened, to
speed up the load time when it is opened in the future. Others are
experiencing this too.
One workaround you could try is, before opening the
Hi Norhan, if your goal is to do a progressiveMauve alignment on the
command-line, your best bet will be a command like this:
./progressiveMauve --output=fifty_isolates.alignment
Autumn2013_ALT_17.gbk Spring2012_ALT_27.gbk
there's no need to use mauveAligner to make an identity matrix for
Hi all,
Following on from this thread, I believe the underlying problem
described may have been the same issue (an incompatibility with the new
boost libraries used by Mauve) that was causing crashes on other
platforms, and that was discussed in a separate thread. I have now been
able to post
Hi Karen,
I presume you're running this on a Mac? What version of the OS are you
running, and have you adjusted the security settings to allow unsigned
applications to run? Mauve 2.3.1 was released before OS X became stingy
about requiring apps to be cryptographically signed. You might try the
Hi Amarin, I realize this reply is coming a bit late but hopefully
better late than never. There was a nasty bug in 2.4.0 which caused
frequent crashes. It's fixed in a snapshot release that was made in late
February. I've now linked the snapshot directly from the download page
on the Mauve site:
Hi Norhan,
If you need programmatic access to do automated processing, you can use
the coordinates in the .backbone file to query an annotation file to get
the features at those particular coordinates. Probably
BioPython/BioPerl/BioJava or some similar API could help with annotation
parsing
Hi Max,
On Wed, 2015-10-14 at 20:45 +, Tagliamonte,Massimiliano S wrote:
> would like to use the resulting files for phylogenetic analyses. I am
> interested in the snapshots xmfa2maf and stripsubsetLCB. I am not sure
> I have a clear idea of what they do, how to use them or which folder
>
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
Hi Susan,
On Tue, 2015-12-08 at 20:05 +, 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
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
>
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:
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
Hi Susan,
On Thu, 2015-11-19 at 20:52 +, Susan Beth Fogelson wrote:
> I am using Mauve to align approximately 35 bacterial genomes to a
> reference. Currently I am using a desktop computer with 16GB of RAM.
> I started the alignment about 2 days ago and it is still running, is
> this a
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
-0500, Amarin Cogburn wrote:
> 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
> <aaron.darl..
Hi Dan,
When the reorderer module runs, it creates a series of folders called
alignmentN inside the chosen output location. These contain successive
runs of the reordering algorithm, which continues either until the
contig ordering converges or a defined limit on the number of iterations
is
Hello Hongxian,
Where/how did you obtain those GBK files? Downloads from the NCBI web
site in GBK format can fail to include the actual genome sequence. Can
you check whether your gbk files have the actual nucleotide sequence at
the end? The file sizes should each be around 9Mb for those two
Hi Lynda, have you tried using the xmfa2maf program that is part of the
Mauve codebase? A build for linux is available here:
http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux-x64/xmfa2ma
f.bz2
to run one must first do:
bunzip2 xmfa2maf
chmod 755 xmfa2maf
If you've already tried that
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
Hi Christine,
There are two levels of the algorithm to consider when it comes to
ambiguities. The first is the alignment anchoring, which is using
spaced seeds to find strings of gap-free matches among the input
sequences. For this, the sequences become encoded in a two-bit
representation, e.g. 00
Hi LiXiang,
The time complexity of the progressiveMauve algorithm scales at least
cubically in the number of genomes being aligned, with length being an
additional approximately n log n factor. In practice that means that
the upper limit for progressiveMauve is usually datasets of around 30-
50
Hi Thierry, good question about the gap file & column headers.
The first columns are as described by the file headers. The subsequent
columns come in triplets, one triplet for each aligned genome,
containing the following information:
1. The genomic position of the gap
2. The name of the
Hi Aleksander,
No the guide tree is not used in the SNP extraction. Did your
progressiveMauve run generate the .backbone and .bbcols files?
Are you generating the SNP file from the command line or within the
viewer? Are there any messages in either the terminal or the console
log window?
Best,
Hi Eugeni,
Before the malloc error, the aligner issued a warning message about the
file CAG00011_hs9.9_v3.fna, which contains characters or formatting
that the software was not expecting in a FastA file. I suggest
carefully checking that file first.
-Aaron
On Mon, 2017-01-09 at 10:44 +0100, Eugeni
Hi Nisha,
I notice in your screenshot that the genomes are labeled with "(no
annotations loaded)".
That means the viewer was unable to find and read the original sequence
file that was aligned.
This can happen if the files are moved around from their location after
alignment, especially if the
/68085883
> email:
> gmarg...@gmail.com
> gabriele.mar...@lgl.bayern.de
>
>
> Von: Aaron Darling [mailto:aaron.darl...@uts.edu.au]
> Gesendet: Dienstag, 11. April 2017 11:28
> An: mauve-users@lists.sourceforge.net
> Betreff: Re: [Mauve-users] Mauve alignment not running
Hi Femi,
The error std::bad_alloc occurs in C++ programs when there is not
enough RAM in the machine to satisfy a memory allocation request.
I notice you are attempting an alignment of three genomes each around
2.3GB in size. It is likely that progressiveMauve will need a machine
with several
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