mummer-help — For general MUMmer questions and help.

[MUMmer-help] promer error “prepro -r returned non-zero”

[Fawn S. <dre...@gm...>]

Hello, all,

I got the error when using promer:
20130522|184556|  4358| ERROR: prepro -r returned non-zero

Any one has an idea?

[MUMmer-help] Could I get a fasta consensus file from the nucmer output?

[Rodrigo De p. B. <rp...@ug...>]

Hi,

I ran Nucmer and I've got my alignment, could I get the consensus fasta file from these alignment?
If yes, how?

Thanks

Rodrigo

[MUMmer-help] Quick question

[Toral, M. <to...@mi...>]

Hello,

I am currently trying to run a mummer report comparing two whole genomes
between two organisms, but keep running into an early error.

Following the basic instructions in the mummer tutorial, I uploaded the two
fasta format genbank full genome files for the two organisms in question,
to use in the initial formation of the promer.delta file, but after I enter
the input:

"promer -p promer genome1.fasta genome2.fasta"

I receive the error:

"ERROR: prepro -r returned non-zero"

Any suggestions on how to fix this problem would be much appreciated!

Thank you,

Marc

Re: [MUMmer-help] Fwd: Wrong Mummerplot behavior [Solved]

[Adam P. <aph...@gm...>]

Thanks Edans, I've checked in a change switches s+ to s* for both the 3 and
4-column mummer formats.

-Adam


On Fri, Mar 22, 2013 at 11:15 PM, Edans Sandes <eda...@gm...>wrote:

> Problem:
>
> > mummerplot -c -x '[0,62190000]' -y '[0,63300000]' -postscript chr5.mu
> gnuplot 4.0 patchlevel 0
> Reading mummer file chr5.mu (use mummer -c)
> ERROR: Could not parse chr5.mu
> 10000348 8549105 32
>
>
> To allow sequences greater than 10.000.000 MBP, please, change Line
> 575 of mummerplot.pl
>
> FROM
>
>  if ( /^\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {
>
> TO
>
>  if ( /^\s*(\S+)\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {
>
> Regards.
> Edans Sandes
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

[MUMmer-help] error when using the whole genome, no error when split it (nucmer)

[Seyed M. <smi...@uc...>]

Hello

I have some difficulties for using nucmer to map two plant genomes against
each other. I first tried to map all the query contigs against all the
reference contigs and it generated error after a while ( during the dot
production phase).  I split the reference to two files, each of them
consists of half of the contigs and mapped the query against them
separately. This time it worked very well.
The original reference file has about 40,000 contigs and total length of
them is about 500,000,000 bps.  The query has about 2,000 contigs and its
total length is almost half of the length of the reference. I used nucmer
with its default parameters and run it on a computer with a huge memory.
Can you help me find the possible sources of the error?

Thank you.

[MUMmer-help] Fwd: Wrong Mummerplot behavior [Solved]

[Edans S. <eda...@gm...>]

Problem:

> mummerplot -c -x '[0,62190000]' -y '[0,63300000]' -postscript chr5.mu
gnuplot 4.0 patchlevel 0
Reading mummer file chr5.mu (use mummer -c)
ERROR: Could not parse chr5.mu
10000348 8549105 32


To allow sequences greater than 10.000.000 MBP, please, change Line
575 of mummerplot.pl

FROM

 if ( /^\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {

TO

 if ( /^\s*(\S+)\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {

Regards.
Edans Sandes

[MUMmer-help] Question about defined(%hash) is deprecated!

[LiuHailan <lh...@ho...>]

Dear Adam Phillippy,
When I used mummerplot to draw graphic based on 
your example (H_pylori26695_Eslice.fasta, H_pyloriJ99_Eslice.fasta), I 
meet some confusing sentences. as follows:

lhl@tw2:~/Desktop/Mummer$ mummerplot -x "[0,275287]" -y "[0,265111]" -postscript -p mummer 1.mums
defined(%hash) is deprecated at /home/lhl/Desktop/MUMmer3.23/mummerplot line 884.
    (Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/lhl/Desktop/MUMmer3.23/mummerplot line 894.
    (Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/lhl/Desktop/MUMmer3.23/mummerplot line 981.
    (Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/lhl/Desktop/MUMmer3.23/mummerplot line 991.
    (Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/lhl/Desktop/MUMmer3.23/mummerplot line 1034.
    (Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/lhl/Desktop/MUMmer3.23/mummerplot line 1044.
    (Maybe you should just omit the defined()?)
gnuplot 4.4 patchlevel 3
Reading mummer file 1.mums (use mummer -c)
Writing plot files mummer.fplot, mummer.rplot
Writing gnuplot script mummer.gp
Rendering plot mummer.ps


I can get a plot, but could you tell me the explation of sentences about "defined(%hash) is deprecated at /home/lhl/Desktop/MUMmer3.23/mummerplot line 884, 894, 981, 991, 1034, and 1044. (Maybe you should just omit the defined()?)" ?  I wonder if it will influence the result. Thank you very much! 

Best regards,
Hailan 		 	   		  

[MUMmer-help] install abort

[Vladimir Y. <ya...@gm...>]

Hello,

For unclear reason installation of MUMmer 3.23 on 64bit RHEL58 aborted
with error. Here is partial output, everything before that seems
completed OK:

make[1]: Leaving directory
`/home/yaximik/Bioinformatics/MUMmer3.23/src/kurtz'
cd /home/yaximik/Bioinformatics/MUMmer3.23/src/tigr; make all
make[1]: Entering directory
`/home/yaximik/Bioinformatics/MUMmer3.23/src/tigr'
/usr/bin/g++ -O3 tigrinc.cc -c -o tigrinc.o
/usr/bin/g++ -O3 annotate.cc tigrinc.o
-o /home/yaximik/Bioinformatics/MUMmer3.23/annotate; chmod
755 /home/yaximik/Bioinformatics/MUMmer3.23/annotate
/usr/bin/g++ -O3 combineMUMs.cc tigrinc.o
-o /home/yaximik/Bioinformatics/MUMmer3.23/combineMUMs; chmod
755 /home/yaximik/Bioinformatics/MUMmer3.23/combineMUMs
/usr/bin/g++ -O3 delta.cc -c -o delta.o
/usr/bin/g++ -O3 delta-filter.cc tigrinc.o delta.o
-o /home/yaximik/Bioinformatics/MUMmer3.23/delta-filter; chmod
755 /home/yaximik/Bioinformatics/MUMmer3.23/delta-filter
/usr/bin/g++ -O3 gaps.cc tigrinc.o
-o /home/yaximik/Bioinformatics/MUMmer3.23/gaps; chmod
755 /home/yaximik/Bioinformatics/MUMmer3.23/gaps
/usr/bin/g++ -O3 mgaps.cc tigrinc.o
-o /home/yaximik/Bioinformatics/MUMmer3.23/mgaps; chmod
755 /home/yaximik/Bioinformatics/MUMmer3.23/mgaps
/usr/bin/g++ -O3 sw_align.cc -c -o sw_align.o
/usr/bin/g++ -O3 postnuc.cc tigrinc.o sw_align.o
-o /home/yaximik/Bioinformatics/MUMmer3.23/aux_bin/postnuc; chmod
755 /home/yaximik/Bioinformatics/MUMmer3.23/aux_bin/postnuc
/usr/bin/ld: cannot open output
file /home/yaximik/Bioinformatics/MUMmer3.23/aux_bin/postnuc: No such
file or directory
collect2: ld returned 1 exit status
chmod: cannot access
`/home/yaximik/Bioinformatics/MUMmer3.23/aux_bin/postnuc': No such file
or directory
make[1]: *** [postnuc] Error 1
make[1]: Leaving directory
`/home/yaximik/Bioinformatics/MUMmer3.23/src/tigr'
make: *** [tigr] Error 2
[yaximik@G5NNJN1 MUMmer3.23]$

What could be the problem?

Vladimir

Re: [MUMmer-help] Error message with PROMER and NUCMER

[Adam P. <aph...@gm...>]

Hi Andy,
That error is usually caused by something trivial. If you can send me
your input files I'd be happy to take a look--they don't look very
large.

-Adam

On Tue, Jan 29, 2013 at 2:16 PM, Andy King <and...@yo...> wrote:
> Hi
>
> I am trying to run both nucmer and promer commands on two files.  The
> reference file contains a single contig.  The query file contains multiple
> contigs.
>
> I keep getting the following error message;
>
> 1: PREPARING DATA
> 2,3: RUNNING mummer AND CREATING CLUSTERS
> # reading input file "promer.aaref" of length 1389932
> # construct suffix tree for sequence of length 1389932
> # (maximum reference length is 536870908)
> # (maximum query length is 4294967295)
> # process 13899 characters per dot
> #....................................................................................................
> # CONSTRUCTIONTIME /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer
> promer.aaref 0.56
> # reading input file "promer.aaqry" of length 840869
> # matching query-file "promer.aaqry"
> # against subject-file "promer.aaref"
> # COMPLETETIME /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer promer.aaref
> 1.01
> # SPACE /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer promer.aaref 2.16
> 4: FINISHING DATA
> Jcr4S000
> ERROR: Could not parse input from 'Query File'.
> Please check the filename and format, or file a bug report
> ERROR: postpro returned non-zero
>
>
> the mummer command works fine.
>
> Thanks
>
> Andy
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

Re: [MUMmer-help] Adding icons to MUMmerplot output

[Adam P. <aph...@gm...>]

Hi Adam T.,
It's relatively easy to edit the gnuplot script (the .gp file
generated by mummerplot). The format is pretty self explanatory. You
can add some lines or points to that file and then generate the plot
by running gnuplot yourself on the .gp file. However, when you are
displaying an alignment of a multi-fasta file, the mummerplot script
takes care of translating the coordinate systems. For example, if you
have 2 contigs on the X-axis, mummerplot lays the second contig out on
the right of the first by simply adding the length of the first contig
to all the match coordinates of the second contig. If you want to plot
arbitrary features, you would either have to do this translation
yourself or hack the mummerplot script to take your features as input.

It's definitely a feature that's on my radar. I started working on a
mummerplot replacement (that supported .gff features) a few years back
but ran out of time and never finished. Will keep this in mind if I
ever pick it back up again.

Best,
-Adam P.


On Wed, Jan 23, 2013 at 5:53 AM, ADAM PAUL TARANTO
<apt...@st...> wrote:
> Does anyone know how to highlight the location of a sequence feature in MUMmerplot output?
>
> I am investigating an expanded gene family, paralogues occur on a number of different scaffolds. I have done an all against all comparison with Promer to identify syntenic regions around the duplicated genes, which was then visualised using mummerplot.
>
> It is difficult to tell where exactly paralogues occur in the graphic generated - So I would like to either A) add markers to the X/Y axises as a visual aide, or B) have mummerplot draw a mark where my gene occurs in self-self scaffold comparisons.
>
> Is it possible to achieve this by manually editing the gnu-plot script or .ps file output by MUMmerplot?
>
> Thanks,
>
> Adam
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help

[MUMmer-help] Error message with PROMER and NUCMER

[Andy K. <and...@yo...>]

Hi

I am trying to run both nucmer and promer commands on two files.  The
reference file contains a single contig.  The query file contains multiple
contigs.

I keep getting the following error message;
*
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "promer.aaref" of length 1389932
# construct suffix tree for sequence of length 1389932
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 13899 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer
promer.aaref 0.56
# reading input file "promer.aaqry" of length 840869
# matching query-file "promer.aaqry"
# against subject-file "promer.aaref"
# COMPLETETIME /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer
promer.aaref 1.01
# SPACE /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer promer.aaref 2.16
4: FINISHING DATA
Jcr4S000
ERROR: Could not parse input from 'Query File'.
Please check the filename and format, or file a bug report
ERROR: postpro returned non-zero
*

the mummer command works fine.

Thanks

Andy

Re: [MUMmer-help] MUMmer's issue with overlapping alignments (request for help)

[Adam P. <aph...@gm...>]

Hi,
Yes, that's a known bug in how nucmer extends alignments. There is a
workaround in the latest release. You can run it like so:

> nucmer --maxmatch --banded -D 10 ref.fasta qry.fasta

This will force nucmer to break an alignment at an indel >10 bp. You
can adjust the -D value to the size of an indel you want included in
the alignment. Although setting it too high is pointless, because
alignments will start terminating due to poor alignment scores.

I believe this should fix the problem. Let me know if it doesn't.

Best,
-Adam


On Thu, Jan 24, 2013 at 7:13 PM, PLD <pla...@gm...> wrote:
> Dear all,
> May I ask for your advice please?
>
> At one point, when I was aligning a reference (NC_010079) to a set of
> contigs, MUMmer recognizes two overlapping alignments:
> 1873926    1902489    65901    37311    28564    28591    99.90    2872915
> 65901    0.99    43.38    NC_010079    contig_64
> 1882538    1939799    57289    1    57262    57289    99.93    2872915
> 65901    1.99    86.93    NC_010079    contig_64
>
> And consequently, dnadiff marks this as GAP:
> contig_64    GAP    57290    37310    -19979    -19952    -27
>
> As this is not what I expected, I tried checking the same region using
> Blast.
> I found that Blast saw this case as a single alignment (instead of two
> overlapping ones):
> contig_64    NC_010079    99.92    65902    26    16    1    65901
> 1939799    1873926    0    1.21E+05
>
> Could this be one example of a known problem that you described on the
> MUMmer 3 manual?
> "nucmer, promer and run-mummer3 all have a difficult time with tandem
> repeats. If the two sequences contain a different number of copies of the
> same tandem repeat, these alignment routines will sometimes generate a
> cluster on either side of the tandem and extend alignments past one another,
> failing to join them into a single alignment region. This generates two
> overlapping alignments and makes it difficult to determine what caused this
> erratic behavior."
> (http://newmbcrr.dfci.harvard.edu/mummer/index.html#nucmer)
>
> If so, may I know if you have advice on fixing this please? Is there any
> parameter that I can change to make MUMmer's results in this case resembles
> Blast's results above?
>
> I would really appreciate your help. Thank you very, very much for your
> time!
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

[MUMmer-help] MUMmer's issue with overlapping alignments (request for help)

[PLD <pla...@gm...>]

Dear all,
May I ask for your advice please?

At one point, when I was aligning a reference (NC_010079) to a set of
contigs, MUMmer recognizes two overlapping alignments:
1873926    1902489    65901    37311    28564    28591    99.90
2872915    65901    0.99    43.38    NC_010079    contig_64
1882538    1939799    57289    1    57262    57289    99.93    2872915
65901    1.99    86.93    NC_010079    contig_64

And consequently, dnadiff marks this as GAP:
contig_64    GAP    57290    37310    -19979    -19952    -27

As this is not what I expected, I tried checking the same region using
Blast.
I found that Blast saw this case as a single alignment (instead of two
overlapping ones):
contig_64    NC_010079    99.92    65902    26    16    1    65901
1939799    1873926    0    1.21E+05

Could this be one example of a known problem that you described on the
MUMmer 3 manual?
"nucmer, promer and run-mummer3 all have a difficult time with tandem
repeats. If the two sequences contain a different number of copies of the
same tandem repeat, these alignment routines will sometimes generate a
cluster on either side of the tandem and extend alignments past one
another, failing to join them into a single alignment region. This
generates two overlapping alignments and makes it difficult to determine
what caused this erratic behavior."
(http://newmbcrr.dfci.harvard.edu/mummer/index.html#nucmer)

If so, may I know if you have advice on fixing this please? Is there any
parameter that I can change to make MUMmer's results in this case resembles
Blast's results above?

I would really appreciate your help. Thank you very, very much for your
time!

[MUMmer-help] Adding icons to MUMmerplot output

[ADAM P. T. <apt...@st...>]

Does anyone know how to highlight the location of a sequence feature in MUMmerplot output? 

I am investigating an expanded gene family, paralogues occur on a number of different scaffolds. I have done an all against all comparison with Promer to identify syntenic regions around the duplicated genes, which was then visualised using mummerplot. 

It is difficult to tell where exactly paralogues occur in the graphic generated - So I would like to either A) add markers to the X/Y axises as a visual aide, or B) have mummerplot draw a mark where my gene occurs in self-self scaffold comparisons. 

Is it possible to achieve this by manually editing the gnu-plot script or .ps file output by MUMmerplot?

Thanks, 

Adam

Re: [MUMmer-help] standard input for repeat-match

[Lee K. <ls...@gm...>]

Hey, it works!  Good trick!  Thanks!


On Mon, Jan 21, 2013 at 3:42 PM, Adam Phillippy <aph...@gm...>wrote:

> Hey Lee,
> Not my program, but I checked the code and it requires a file name on the
> command line. You may be able to trick it by doing:
>
> > repeat-match /dev/stdin
>
> Best,
> -Adam
>
>
> On Tue, Jan 8, 2013 at 9:46 PM, Lee Katz <ls...@gm...> wrote:
>
>> is it possible to do standard input for repeat-match?  I have a script
>> where I am running it many times in multiple threads, and I think it is
>> slowing my script because of hard drive IO.  I am hoping that it will be
>> faster to do something like
>>
>> #!/usr/bin/env perl
>> $repeat=`echo 'AAAAATTAAAAA' | repeat-match -n 4 -t -E | tail -n +3 |
>> sort -k1,1n -k2,2n`
>>
>> One more thing is that I tried this CLI trick, but it didn't work (not
>> really sure what I expected to happen)
>> $ perl -e '`repeat-match -n 4 -t -E <(echo "AAAAATTAAAAA")`'
>>
>> This does work though
>> $ repeat-match -n 4 -E -t <(echo "AAAAATTCAAAAA") # no results though
>>
>> Thank you for your help!
>>
>> --
>> Lee Katz, Ph.D.
>>
>>
>> ------------------------------------------------------------------------------
>> Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery
>> and much more. Keep your Java skills current with LearnJavaNow -
>> 200+ hours of step-by-step video tutorials by Java experts.
>> SALE $49.99 this month only -- learn more at:
>> http://p.sf.net/sfu/learnmore_122612
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li...
>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>>
>


-- 
Lee Katz, Ph.D.

Re: [MUMmer-help] Trouble with 'Assertion `Len > 0 && Line [Len - 1] == '\n'' failed.' Error

[Adam P. <aph...@gm...>]

Hi John,
Sometimes I see this error when the input fasta file has a formatting error
-- most commonly when two records in the same file share the same
identifier. The identifier is the string taken from the '>' up to the first
whitespace. Make sure all the records in your input have unique IDs and try
again.

Best,
-Adam

On Wed, Jan 16, 2013 at 3:40 PM, John F Wolters <jwo...@bi...>wrote:

> COXICDS

Re: [MUMmer-help] standard input for repeat-match

[Adam P. <aph...@gm...>]

Hey Lee,
Not my program, but I checked the code and it requires a file name on the
command line. You may be able to trick it by doing:

> repeat-match /dev/stdin

Best,
-Adam


On Tue, Jan 8, 2013 at 9:46 PM, Lee Katz <ls...@gm...> wrote:

> is it possible to do standard input for repeat-match?  I have a script
> where I am running it many times in multiple threads, and I think it is
> slowing my script because of hard drive IO.  I am hoping that it will be
> faster to do something like
>
> #!/usr/bin/env perl
> $repeat=`echo 'AAAAATTAAAAA' | repeat-match -n 4 -t -E | tail -n +3 | sort
> -k1,1n -k2,2n`
>
> One more thing is that I tried this CLI trick, but it didn't work (not
> really sure what I expected to happen)
> $ perl -e '`repeat-match -n 4 -t -E <(echo "AAAAATTAAAAA")`'
>
> This does work though
> $ repeat-match -n 4 -E -t <(echo "AAAAATTCAAAAA") # no results though
>
> Thank you for your help!
>
> --
> Lee Katz, Ph.D.
>
>
> ------------------------------------------------------------------------------
> Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery
> and much more. Keep your Java skills current with LearnJavaNow -
> 200+ hours of step-by-step video tutorials by Java experts.
> SALE $49.99 this month only -- learn more at:
> http://p.sf.net/sfu/learnmore_122612
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] standard input for repeat-match

[Lee K. <ls...@gm...>]

is it possible to do standard input for repeat-match?  I have a script
where I am running it many times in multiple threads, and I think it is
slowing my script because of hard drive IO.  I am hoping that it will be
faster to do something like

#!/usr/bin/env perl
$repeat=`echo 'AAAAATTAAAAA' | repeat-match -n 4 -t -E | tail -n +3 | sort
-k1,1n -k2,2n`

One more thing is that I tried this CLI trick, but it didn't work (not
really sure what I expected to happen)
$ perl -e '`repeat-match -n 4 -t -E <(echo "AAAAATTAAAAA")`'

This does work though
$ repeat-match -n 4 -E -t <(echo "AAAAATTCAAAAA") # no results though

Thank you for your help!

-- 
Lee Katz, Ph.D.

[MUMmer-help] Help required for installation of MUMmer 3.23 software

[Kamal K. P. <kkp...@gm...>]

Sir

Please update me about the following

1. Whether the MUMmer 3.23 version can be operated and installed in CentOS
5.4 verion of Lunix system with 32 bit system
2. Whether MUMmer~.rpm is available
3. Please suggest other alternatives

Thanks and regards,

K K Pal

-- 
Dr. K. K. Pal
Principal Scientist, Microbiology
Directorate of Groundnut Research
Ivnagar Road, PB No. 5, Junagadh-362001
Gujarat
Fax:02852672550
Tel:0285-2673041/2672461 ext 138/139
Res. 0285-2673274
Mob:09426476749
E-mail:kkp...@gm...
kam...@ya...
pa...@nr...

[MUMmer-help] How to run Mummer using multiple threads

[Jiao, Y. <yj...@cs...>]

Hi,

Is there any possible to run "nucmer" by multiple threads.
I can't find it in the manual.
Thank you!

Yinping

Re: [MUMmer-help] Data directory

[Yosi M. <yos...@gm...>]

Hi Adam,

Thank you for your help.

Yosi

On Tue, Dec 18, 2012 at 11:21 AM, Adam Phillippy <aph...@gm...>wrote:

> Hi Yosi,
> SourceForge is in the process of reorganizing, and this seems to have
> broken the web hosting. Until I can fix the problem, I've temporarily
> rehosted these files for you here:
>
> ftp://ftp.cbcb.umd.edu/pub/software/mummer/examples/data
>
> Best,
> -Adam
>
> On Thu, Dec 13, 2012 at 10:06 AM, Yosi Maruvka <yos...@gm...>wrote:
>
>> Hello,
>>
>> I installed you program, and wanted to learn how to use it, via your
>> examples, however the link to the data directory<http://mummer.sourceforge.net/examples/data> ,as
>> referred in the examples page <http://mummer.sourceforge.net/examples/>  is
>> broken.
>>
>> Is there another way that I can get this data from?
>>
>> Thanks,
>>
>> Yosi
>>
>>
>> ------------------------------------------------------------------------------
>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>> Remotely access PCs and mobile devices and provide instant support
>> Improve your efficiency, and focus on delivering more value-add services
>> Discover what IT Professionals Know. Rescue delivers
>> http://p.sf.net/sfu/logmein_12329d2d
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li...
>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>>
>

Re: [MUMmer-help] Data directory

[Adam P. <aph...@gm...>]

Hi Yosi,
SourceForge is in the process of reorganizing, and this seems to have
broken the web hosting. Until I can fix the problem, I've temporarily
rehosted these files for you here:

ftp://ftp.cbcb.umd.edu/pub/software/mummer/examples/data

Best,
-Adam

On Thu, Dec 13, 2012 at 10:06 AM, Yosi Maruvka <yos...@gm...>wrote:

> Hello,
>
> I installed you program, and wanted to learn how to use it, via your
> examples, however the link to the data directory<http://mummer.sourceforge.net/examples/data> ,as
> referred in the examples page <http://mummer.sourceforge.net/examples/>  is
> broken.
>
> Is there another way that I can get this data from?
>
> Thanks,
>
> Yosi
>
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] Data directory

[Yosi M. <yos...@gm...>]

Hello,

I installed you program, and wanted to learn how to use it, via your
examples, however the link to the data
directory<http://mummer.sourceforge.net/examples/data> ,as
referred in the examples page <http://mummer.sourceforge.net/examples/>  is
broken.

Is there another way that I can get this data from?

Thanks,

Yosi

[MUMmer-help] Reg:Run-mummer3 .align file output

[yuva r. <yuv...@gm...>]

Dear colleague,

I used mummer tool and I found it to be amazing.

Lately,I have been using run-mummer3,I found some information that i need
to be missing.

I performed run-mummer3 for
Saccharomyces_cerevisiae.EF4.13.dna.chromosome.IV fasta sequence and I got
the attached .align file. In .align file for the first region (line no 73
in .align file) from residue no 88 to 898 ,alignment is there but for the
other regions such as regions in line no 75,79,82
,85,88,91,94,97,100,103,106,109 of the .align file,for those regions i want
to see the alignment.how can I get the alignment for these regions.

In specific, for example, for first region residue no (88-898) alignment,it
should start at 88 position but it is starting at 112 th residue..how can i
get whole alignment right from 88 to 898 th residue

Kindly help me in this regard...eagerly waiting for your kind reply.


pls find attachment



Thank you




YUVARAJ.I
Short Term Researcher
Indian Institute Of Science
Banglore.

[MUMmer-help] Parameters for using MUMmer to align a metagenomic assembly against a metagenomic reference

[Ino de B. <ino...@sc...>]

Hello everybody,

I have been using MUMmer to align a metavelvet assembly of Illumina reads against a metagenomic reference of ~60 species.  What I want to assess is how well the assembly covers the reference metagenome. I run nucmer only once with the metavelvet contigs as a query and all the reference genomes of the metagenome combined in one file. So far I have been using only the --maxmatch parameter for nucmer and the default parameters. Afterwards I filter with delta-filter -g, to get the longest mutually consistent set for all reference-query pairs. What I can easily extract then is for each contig how "pure" it is, i.e. the query coverage. The incorrect bases or gaps could come from (1) errors in the sequencing process i.e. misreading bases/contamination, or (2) misassembly where reads belonging to different species have been combined into one species.

What I would like to know is:

- Is just using nucmer --maxmatch with default parameters a good idea for determining this query coverage per contig for metagenomics or do you recommend other parameters? 

- When using delta-filter -g, what if the longest mutually consistent is equal for a query against two genomes in the reference metagenome e.g. a query that represents a shared region. Are both alignments outputted in that case or is simply one chosen randomly? It doesn't matter for determining the query coverage, since they will be equal, but it would be interesting to know.

- How does the extension step work exactly, I understand Smith-Waterman is used and that --breaklen allows you to specify when it should stop trying to extend the alignment in case of a negatively scoring aligment (right?), but what are the substitution and gap scoring schemes applied? And how does that relate to the alignment identity? At what minimum identity score is the extension stopped? Maybe I should read the articles better but I couldn't really find that.

- I would also like to know how much of each genome in the reference metagenome is covered by the contigs. What would be a good way to do this? Maybe delta-filter -r, sort on reference genome with show-coords -r and count the non-overlapping bases? I reckon this would include repeats since I choose --maxmatch and it would be no problem for shared regions between genomes either since delta-filter -r checks for the longest consistent match per reference genome. Or should I not do any delta-filtering at all? I guess I don't really understand what -r does, does it only remove query sequences that overlap?

Hope someone can help and thanks a lot for making the software, it's great!

Best regards,
Ino de Bruijn