mummer-help — For general MUMmer questions and help.

Re: [MUMmer-help] deltafilter -q (was: overlapping matches when calling mummer -mum)

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

delta-filter -q will only discard alignments that are fully contained by a
better alignment on the query. Alignments that overlap, but each contain
some unique sequence, will be kept.

-Adam


On Tue, Nov 3, 2015 at 3:31 PM, Afif Elghraoui <ael...@sd...> wrote:

> Hi, Adam,
>
> On 11/03/2015 12:05 PM, Adam Phillippy wrote:
>
> Nucmer alignments will often overlap for the same reason MUMs can overlap
> (repeats). In the example you give the alignments overlap on the reference,
> but they do not overlap on the query. delta-filter -q tries to find the
> best alignments that cover as much of the query sequence as possible. Thus,
> this little 714 bp sequence appears duplicated in your query, but not your
> reference. delta-filter keeps it because it explains positions 3744105-3744818
> on the query.
>
>
> I understood that one, but I was referring to the middle line. Here is the
> snippet again:
>
> 3569553 3701911 3570622 *3702980* 132359  132359  99.99   4419977 4425991
> 2.99    2.99 ...
> 3701734 3741905 *3702919* 3743090 40172   40172   99.98   4419977 4425991
> 0.91    0.91 ...
> 3741192 3741905 3744105 3744818 714     714     98.60   4419977 4425991
> 0.02    0.02 ...
>
> The actual positions 3702919-3702980 in the query overlap in the first and
> second lines. I understand why the alignment is overlapping, but shouldn't delta-filter
> -q have filtered out the alignment corresponding to the second line here?
> In other words, is delta-filter -q *supposed* to throw out all alignments
> that result in query overlaps?
>
>
> I promise you will find many similar examples as you continue to play with
> the data. These types of alignments are very common when aligning
> assemblies to references (due either to mis-assembly or true variants), and
> sorting them all out is a very difficult problem.
>
> Of course.
>
> Many thanks and regards
> Afif
>
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

Re: [MUMmer-help] deltafilter -q (was: overlapping matches when calling mummer -mum)

[Afif E. <ael...@sd...>]

Hi, Adam,

On 11/03/2015 12:05 PM, Adam Phillippy wrote:
> Nucmer alignments will often overlap for the same reason MUMs can 
> overlap (repeats). In the example you give the alignments overlap on 
> the reference, but they do not overlap on the query. delta-filter -q 
> tries to find the best alignments that cover as much of the query 
> sequence as possible. Thus, this little 714 bp sequence appears 
> duplicated in your query, but not your reference. delta-filter keeps 
> it because it explains positions 3744105-3744818 on the query.

I understood that one, but I was referring to the middle line. Here is 
the snippet again:

3569553 3701911 3570622 *3702980* 132359  132359  99.99  4419977 
44259912.99    2.99 ...
3701734 3741905 *3702919* 3743090 40172   40172   99.98  4419977 
44259910.91    0.91 ...
3741192 3741905 3744105 3744818 714     714     98.60   4419977 
44259910.02    0.02 ...

The actual positions 3702919-3702980 in the query overlap in the first 
and second lines. I understand why the alignment is overlapping, but 
shouldn't delta-filter -q have filtered out the alignment corresponding 
to the second line here? In other words, is delta-filter -q /supposed/ 
to throw out all alignments that result in query overlaps?

>
> I promise you will find many similar examples as you continue to play 
> with the data. These types of alignments are very common when aligning 
> assemblies to references (due either to mis-assembly or true 
> variants), and sorting them all out is a very difficult problem.
>
Of course.

Many thanks and regards
Afif

Re: [MUMmer-help] overlapping matches when calling mummer -mum

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

Hi Afif,
Nucmer alignments will often overlap for the same reason MUMs can overlap
(repeats). In the example you give the alignments overlap on the reference,
but they do not overlap on the query. delta-filter -q tries to find the
best alignments that cover as much of the query sequence as possible. Thus,
this little 714 bp sequence appears duplicated in your query, but not your
reference. delta-filter keeps it because it explains positions 3744105-3744818
on the query.

I promise you will find many similar examples as you continue to play with
the data. These types of alignments are very common when aligning
assemblies to references (due either to mis-assembly or true variants), and
sorting them all out is a very difficult problem.

Best,
-Adam


On Mon, Nov 2, 2015 at 7:01 PM, Afif Elghraoui <ael...@sd...> wrote:

> Hi, Adam,
> Thanks for your prompt response. Please see below inline--
>
> On 11/02/2015 02:56 PM, Adam Phillippy wrote:
> > This is the intended behavior of the program. I believe you are
> > misinterpreting the meaning of a maximal unique match. A maximal match
> > is defined as a match that cannot be extended on either end without
> > encountering a mismatch. Just because a MUM contains a repetitive
> > sequence, does not make the whole MUM non-unique. For the two
> > sequences with unique seqs 'U' and tandem repeats 'T':
> >
> > A: UUUTTTUUU
> > B: UUUTTUUU
> >
> > There would be MUMs found on either side: UUUTT and TTUUU. These two
> > MUMs overlap on both T's in B and overlap on the middle T in A. Both
> > MUMs are unique, i.e. they don't appear anywhere else as a whole ...
> > though they do contain substrings that are repetitive. I hope this
> > little example makes it a little more clear.
>
> Yes, thanks. That makes it clear.
>
> > Nucmer or dnadiff are the best tools in MUMmer for comparing contigs
> > to a reference. I prefer to run:
> > > nucmer -maxmatch -banded ref.fna. contigs.fna
> > > delta-filter -q out.delta > out.qdelta
> > > show-coords -THrcl out.qdelta > out.coords
> >
> > This will report the best alignments found for each contig to the
> > reference, which you can parse to identify large differences or run
> > show-snps to identify smaller polymorphisms.
> >
>
> I have a single contig, but I've already tried these before I switched
> to the plain mummer program. These are the various settings I used for
> nucmer: (Some of these parameter settings were chosen based on my
> mistaken understanding of a MUM)
>
> nucmer01/Makefile:NUCMER = nucmer --maxmatch --banded -D 10
> nucmer02/Makefile:NUCMER = nucmer --mumreference --banded -D 10
> nucmer03/Makefile:NUCMER = nucmer --mum --banded -D 10
> nucmer04/Makefile:NUCMER = nucmer --maxmatch --banded -D 5
> nucmer05/Makefile:NUCMER = nucmer -c 40
> nucmer06/Makefile:NUCMER = nucmer --maxmatch --banded -D 10 -c 40
> nucmer07/Makefile:NUCMER = nucmer --maxmatch
> nucmer08/Makefile:NUCMER = nucmer --forward
> nucmer09/Makefile:NUCMER = nucmer --banded -D 1
> nucmer10/Makefile:NUCMER = nucmer --noextend
> nucmer11/Makefile:NUCMER = nucmer --noextend --mum
>
> my nucmer04/ attempt matches your example if the default value of -D is
> 5 as the nucmer -help text says. In any case, My out.qcoords
> (show-coords based on delta-filter -q output) for that attempt has these
> corresponding lines:
>
> 3569553 3701911 3570622 3702980 132359  132359  99.99   4419977 4425991
> 2.99    2.99 ...
> 3701734 3741905 3702919 3743090 40172   40172   99.98   4419977 4425991
> 0.91    0.91 ...
> 3741192 3741905 3744105 3744818 714     714     98.60   4419977 4425991
> 0.02    0.02 ...
>
> I thought that delta-filter -q would throw out the alignment
> corresponding to the middle line there since it overlaps another
> alignment on the query. Is delta-filter -q supposed to do that?
>
> Basically, my goal is to break the variant detection (both large and
> small) into steps to get a better handle of it for automatic processing
> of dozens of completed assemblies. For my first step, I want to know
> what exactly should be inserted or deleted from the reference in order
> to transform it into the query. After that, my next step would be to
> process all the differences and annotate/categorize them.
>
> I was apparently able to achieve my first step using plain old Unix diff
> once I appropriately formatted my files for it, though.
>
> Many thanks and regards
> Afif
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

Re: [MUMmer-help] overlapping matches when calling mummer -mum

[Afif E. <ael...@sd...>]

Hi, Adam,
Thanks for your prompt response. Please see below inline--

On 11/02/2015 02:56 PM, Adam Phillippy wrote:
> This is the intended behavior of the program. I believe you are 
> misinterpreting the meaning of a maximal unique match. A maximal match 
> is defined as a match that cannot be extended on either end without 
> encountering a mismatch. Just because a MUM contains a repetitive 
> sequence, does not make the whole MUM non-unique. For the two 
> sequences with unique seqs 'U' and tandem repeats 'T':
>
> A: UUUTTTUUU
> B: UUUTTUUU
>
> There would be MUMs found on either side: UUUTT and TTUUU. These two 
> MUMs overlap on both T's in B and overlap on the middle T in A. Both 
> MUMs are unique, i.e. they don't appear anywhere else as a whole ... 
> though they do contain substrings that are repetitive. I hope this 
> little example makes it a little more clear.

Yes, thanks. That makes it clear.

> Nucmer or dnadiff are the best tools in MUMmer for comparing contigs 
> to a reference. I prefer to run:
> > nucmer -maxmatch -banded ref.fna. contigs.fna
> > delta-filter -q out.delta > out.qdelta
> > show-coords -THrcl out.qdelta > out.coords
>
> This will report the best alignments found for each contig to the 
> reference, which you can parse to identify large differences or run 
> show-snps to identify smaller polymorphisms.
>

I have a single contig, but I've already tried these before I switched 
to the plain mummer program. These are the various settings I used for 
nucmer: (Some of these parameter settings were chosen based on my 
mistaken understanding of a MUM)

nucmer01/Makefile:NUCMER = nucmer --maxmatch --banded -D 10
nucmer02/Makefile:NUCMER = nucmer --mumreference --banded -D 10
nucmer03/Makefile:NUCMER = nucmer --mum --banded -D 10
nucmer04/Makefile:NUCMER = nucmer --maxmatch --banded -D 5
nucmer05/Makefile:NUCMER = nucmer -c 40
nucmer06/Makefile:NUCMER = nucmer --maxmatch --banded -D 10 -c 40
nucmer07/Makefile:NUCMER = nucmer --maxmatch
nucmer08/Makefile:NUCMER = nucmer --forward
nucmer09/Makefile:NUCMER = nucmer --banded -D 1
nucmer10/Makefile:NUCMER = nucmer --noextend
nucmer11/Makefile:NUCMER = nucmer --noextend --mum

my nucmer04/ attempt matches your example if the default value of -D is 
5 as the nucmer -help text says. In any case, My out.qcoords 
(show-coords based on delta-filter -q output) for that attempt has these 
corresponding lines:

3569553 3701911 3570622 3702980 132359  132359  99.99   4419977 4425991 
2.99    2.99 ...
3701734 3741905 3702919 3743090 40172   40172   99.98   4419977 4425991 
0.91    0.91 ...
3741192 3741905 3744105 3744818 714     714     98.60   4419977 4425991 
0.02    0.02 ...

I thought that delta-filter -q would throw out the alignment 
corresponding to the middle line there since it overlaps another 
alignment on the query. Is delta-filter -q supposed to do that?

Basically, my goal is to break the variant detection (both large and 
small) into steps to get a better handle of it for automatic processing 
of dozens of completed assemblies. For my first step, I want to know 
what exactly should be inserted or deleted from the reference in order 
to transform it into the query. After that, my next step would be to 
process all the differences and annotate/categorize them.

I was apparently able to achieve my first step using plain old Unix diff 
once I appropriately formatted my files for it, though.

Many thanks and regards
Afif

Re: [MUMmer-help] overlapping matches when calling mummer -mum

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

Hi Afif,
This is the intended behavior of the program. I believe you are
misinterpreting the meaning of a maximal unique match. A maximal match is
defined as a match that cannot be extended on either end without
encountering a mismatch. Just because a MUM contains a repetitive sequence,
does not make the whole MUM non-unique. For the two sequences with unique
seqs 'U' and tandem repeats 'T':

A: UUUTTTUUU
B: UUUTTUUU

There would be MUMs found on either side: UUUTT and TTUUU. These two MUMs
overlap on both T's in B and overlap on the middle T in A. Both MUMs are
unique, i.e. they don't appear anywhere else as a whole ... though they do
contain substrings that are repetitive. I hope this little example makes it
a little more clear.

Nucmer or dnadiff are the best tools in MUMmer for comparing contigs to a
reference. I prefer to run:
> nucmer -maxmatch -banded ref.fna. contigs.fna
> delta-filter -q out.delta > out.qdelta
> show-coords -THrcl out.qdelta > out.coords

This will report the best alignments found for each contig to the
reference, which you can parse to identify large differences or run
show-snps to identify smaller polymorphisms.

Best,
-Adam


On Mon, Nov 2, 2015 at 2:54 PM, Afif Elghraoui <ael...@sd...> wrote:

> Hello,
> I am trying to get a very basic comparison between a de novo assembled
> microbial genome and a reference sequence. I used nucmer at first, but
> there was a tandem duplication that was causing overlapping alignments
> and I just wanted to know precisely what was different. It appears that
> the plain mummer program would be appropriate for finding this out, so I
> called mummer as follows:
>
> mummer -mum <reference> <query>
>
> By using the -mum flag, I thought that I'm not supposed to be seeing any
> overlap in the matches in both the query and reference, but I found an
> instance of this in those positions where I was previously getting
> overlaps in my nucmer alignments:
>
> 3569553   3570622    132349
> 3701734   3702919     39749
>
> If I understood the format of the output correctly, the first match here
> overlaps the second in the reference (3569553+132349 = 3701902 >
> 3701734) and the query. By manual inspection of blast results of these
> positions, I know that there is a tandem repeat in this region where the
> query has five copies and the reference has three copies and the overlap
> in the matches here matches all three copies in the reference twice and
> also matches one of the copies in the query twice.
>
> This doesn't look to me like intended behavior of the program,
> especially since I'm not using -maxmatch. Am I doing something wrong or
> misunderstanding anything here? I'm using MUMmer 3.23 as packaged in
> Debian 8. I can provide my query genome privately if necessary.
>
> Many thanks and regards
> Afif
>
> --
> Afif Elghraoui
> Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence
> San Diego State University
> Alvarado Medical Center
> 6367 Alvarado Court, Suite 206
> San Diego, CA 92120
> p. 858-222-0454
> http://tuberculosis.sdsu.edu
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

[MUMmer-help] overlapping matches when calling mummer -mum

[Afif E. <ael...@sd...>]

Hello,
I am trying to get a very basic comparison between a de novo assembled 
microbial genome and a reference sequence. I used nucmer at first, but 
there was a tandem duplication that was causing overlapping alignments 
and I just wanted to know precisely what was different. It appears that 
the plain mummer program would be appropriate for finding this out, so I 
called mummer as follows:

mummer -mum <reference> <query>

By using the -mum flag, I thought that I'm not supposed to be seeing any 
overlap in the matches in both the query and reference, but I found an 
instance of this in those positions where I was previously getting 
overlaps in my nucmer alignments:

3569553   3570622    132349
3701734   3702919     39749

If I understood the format of the output correctly, the first match here 
overlaps the second in the reference (3569553+132349 = 3701902 > 
3701734) and the query. By manual inspection of blast results of these 
positions, I know that there is a tandem repeat in this region where the 
query has five copies and the reference has three copies and the overlap 
in the matches here matches all three copies in the reference twice and 
also matches one of the copies in the query twice.

This doesn't look to me like intended behavior of the program, 
especially since I'm not using -maxmatch. Am I doing something wrong or 
misunderstanding anything here? I'm using MUMmer 3.23 as packaged in 
Debian 8. I can provide my query genome privately if necessary.

Many thanks and regards
Afif

-- 
Afif Elghraoui
Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence
San Diego State University
Alvarado Medical Center
6367 Alvarado Court, Suite 206
San Diego, CA 92120
p. 858-222-0454
http://tuberculosis.sdsu.edu

[MUMmer-help] Help with mummerplot

[Arpan B. <arp...@gm...>]

Hi,

I ran nucmer to align a genome scaffold to another genome. I am trying to
use mummerplot to obtain a plot like
http://mummer.sourceforge.net/manual/covplot.gif

The command I am using is

mummerplot -t png -s large -p nuc_UMN1_Scaff1 nuc_UMN1_Scaff1.delta

I am getting this error:

"nuc_UMN1_Scaff1.gp", line 33358: integer overflow; change to floating point

WARNING: Unable to run 'gnuplot nuc_UMN1_Scaff1.gp', Inappropriate ioctl
for device
Do you have any suggestions?

Re: [MUMmer-help] Could not find any alignments while using "show-aligns"

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

Hello,
Try running show-coords first. The last two columns will list the reference
and query sequence IDs. If there is no line in the show-coords output
listing an alignment between 30 and 33, then there are no alignments to
report.

Best,
-Adam


On Fri, Oct 2, 2015 at 6:00 AM, Rameez Mj <ram...@gm...> wrote:

> I am trying to align one draft genome contigs to another draft genome
> contigs.I generated the delta file and proceeded for show-aligns command
> like this
>
> "show-aligns ref_qry.delta -r 30 33 > ref_qry.aligns" where 30 and 33 are
> the names I wish to see in the alignment for both my draft sequences
> respectively. But this commands shows "ERROR: Could not find any alignments
> for 30 and 33". I am not able to resolve this,can anyone help me with
> it.Thanks in advance.
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] Could not find any alignments while using "show-aligns"

[Rameez Mj <ram...@gm...>]

I am trying to align one draft genome contigs to another draft genome
contigs.I generated the delta file and proceeded for show-aligns command
like this

"show-aligns ref_qry.delta -r 30 33 > ref_qry.aligns" where 30 and 33 are
the names I wish to see in the alignment for both my draft sequences
respectively. But this commands shows "ERROR: Could not find any alignments
for 30 and 33". I am not able to resolve this,can anyone help me with
it.Thanks in advance.

Re: [MUMmer-help] ERROR: mummer and/or mgaps returned non-zero

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

Hello,
This error typically occurs when your computer runs out of memory. You can
either switch to a computer with more RAM or divide your genome into parts
and align each separately to cut down on the memory usage.

Best,
-Adam


On Fri, Sep 4, 2015 at 10:34 PM, xiejianbo1860 <xie...@16...>
wrote:

> Dear Professor,
>
> Now i am using mummer to do alignment work, but i met a problem that i
> can't solve.  I will appreciate if you could help me!
>
> Here i describe the error i met, i want to find reliable set of snps in
> ref plant genomes (less than 500M), and it is less than the maximum
> reference length. the error messages are showed as below:
>
> The command : nucmer -maxmatch -c 90 -l 40   --prefix=ref_3 2_ref.fa
> 3_qry.fa
>
> # reading input file "ref_3.ntref" of length 394507750
> # construct suffix tree for sequence of length 394507750
> # (maximum reference length is 536870908)
> # (maximum query length is 4294967295)
> # process 3945077 characters per dot
> #................................................................................................ERROR:
> mummer and/or mgaps returned non-zero
>
>
> Could you help me to solve this problem?
>
> Best wishes.
>
> Thanks!
>
> No.35 Qinghua East Road, Haidian District
> BEIJING 100083
> P.R.CHINA
>
>
>
>
>
>
> 2015-09-05
> ------------------------------
> xiejianbo1860
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] ERROR: mummer and/or mgaps returned non-zero

[xiejianbo1860<xie...@16...>]

Dear Professor,

Now i am using mummer to do alignment work, but i met a problem that i can't solve.  I will appreciate if you could help me!

Here i describe the error i met, i want to find reliable set of snps in ref plant genomes (less than 500M), and it is less than the maximum reference length. the error messages are showed as below:

The command : nucmer -maxmatch -c 90 -l 40   --prefix=ref_3 2_ref.fa 3_qry.fa

# reading input file "ref_3.ntref" of length 394507750
# construct suffix tree for sequence of length 394507750
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 3945077 characters per dot
#................................................................................................ERROR: mummer and/or mgaps returned non-zero


Could you help me to solve this problem?

Best wishes.

Thanks!
  
No.35 Qinghua East Road, Haidian District
BEIJING 100083
P.R.CHINA 

 




2015-09-05


xiejianbo1860 

Re: [MUMmer-help] delta-filter memory usage

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

Hi Greg,
It is possible that the loaded delta file could consume more memory than
the original file. The file format is different than the data structure
that is built from that file. 9GB is also quite large for a delta file, and
usually an signal to use more conservative alignment parameters, e.g. a
larger seed size, the -mumreference option, larger cluster size, etc.

Best,
-Adam


On Tue, Jul 14, 2015 at 2:03 PM, G. Magoon <gre...@gm...> wrote:

> Hi,
> I have a ~9 GB .delta file that I'm trying to filter with delta-filter
> (MUMmer 3.23) on a computer with 16 GB RAM (+ 4 GB swap space). Within a
> minute or two of launching, the delta-filter process takes up essentially
> the entire system memory and is eventually killed by the system, apparently
> without having produced any output. I'm new to MUMmer, but my naive
> expectation was that it would only need enough memory to store the full
> delta file (at most).
>
> Is this high memory usage expected? If so, is there a way to estimate the
> memory that would be required for the delta-filter process to complete
> successfully?
>
> Thanks very much in advance,
> Greg
>
>
> ------------------------------------------------------------------------------
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[MUMmer-help] Using MUMMER to infer pseudogene intron loss?

[Anand K S R. <ak...@uc...>]

I have not yet used MUMMER for any of my analyses.
Therefore, I seek your help to decide whether MUMMER3.0 can be a suitable
tool for the following *objective*:

Using a 3rd party analysis pipeline, I have generated a set of predicted
pseudogenes - both processed and non-processed.

At the moment, I cannot distinguish these 2 cases. But, my goal is to
identify processed pseudogenes. One way to do this is to compare the number
of introns in pseudogene to that in sister gene.

*Work so far*

I have mapped each predicted pseduogene to its best sister gene. The
pseudogene was identified in the 1st place, using the sister protein as a
tBLASTn query.

*The Objective: Can MUMMER do this?*

I want to know whether MUMMER can align the predicted pseudogene to its
sister gene. Either directly at the DNA sequence level, or via intermediate
steps involving cDNA / protein from the sister gene. Will such an approach
help 'count' the introns in sister gene Vs pseudogene, and thereby help
infer whether a predicted locus may have been generated as a retrogene or
not?

*Info available*

I have the following information at my disposal:
1. Coords and DNA sequence of pseudogene prediction
2. Sister gene DNA sequence
3. Sister gene full-length cDNA sequence
4. Sister gene full-length protein sequence
5. Sister gene protein sub-sequence that matches the pseudogene coords

Thank you all, in advance!

[MUMmer-help] delta-filter memory usage

[G. M. <gre...@gm...>]

Hi,
I have a ~9 GB .delta file that I'm trying to filter with delta-filter
(MUMmer 3.23) on a computer with 16 GB RAM (+ 4 GB swap space). Within a
minute or two of launching, the delta-filter process takes up essentially
the entire system memory and is eventually killed by the system, apparently
without having produced any output. I'm new to MUMmer, but my naive
expectation was that it would only need enough memory to store the full
delta file (at most).

Is this high memory usage expected? If so, is there a way to estimate the
memory that would be required for the delta-filter process to complete
successfully?

Thanks very much in advance,
Greg

Re: [MUMmer-help] MUMmer SNP output data help

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

Hi Ramya,
For draft IonTorrent data, you may be better off using a reference-mapping
approach for SNP calling and work directly from the reads rather than the
assemblies. There are a number of available pipelines for this. By mapping
the reads you could take the quality values of each base into account and
perhaps obtain more accurate SNP calls.

If you are determined to use assemblies, we have a new tool called ParSNP
for comparing multiple samples. Here is the paper if you are interested:
http://www.genomebiology.com/content/15/11/524 That paper also discusses
the tradeoffs between assembly-based and read-based SNP calling.

To directly answer your questions:
1. Yes, but there are probably better options
2. Yes
3. You would align each assembly to the reference individually
4. No, you would have to parse this information yourself from the output

Best,
-Adam


On Wed, Jun 17, 2015 at 8:34 AM, <ra...@bi...> wrote:

> Hi all,
>
> I have been working with Iontorrent platform. I have sequence of a
> bacteria which was obtained by denovo assembly on Ion torrent platform. I
> have to use this data as a reference for calling SNP's across 6 samples. So
> it would be draft genome vs draft genome. I have used the nucmer snp
> caller. My questions are:
>
> 1) can i use this tool for calling SNP's from data generated from
> Iontorrent platform?
>
> 2) Do i need to align the draft sequences first before going to the SNP
> calling option?
>
> 2) Should i cal SNP's from one sample and then compare it with others or
> all the sample's data can be combined and called for SNP's? for example can
> i go with command line
>
> nucmer --prefix=ref_qry ref.fasta sample1.fasta sample2.fasta
> sample.3.fasta
>
> 3) IS there an option to generate unique SNP's to a particular sample and
> common variants across all the samples?
>
> Thanks in advance,
>
>
>
> Ramya.
>
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] mummer issues

[Chunda F. <cf...@ua...>]

Hello experts,

I am using Mummer3.23 to compare the draft genome sequences of two races of the plant pathogen I am working on.  The dot plots generated by mummerplot from my sequences are weird. Can anyone tell me how to fix the problem? Also, I occasionally encountered issues listed below:

1.       tail: cannot open `+3' for reading: No such file or directory

2.       ERROR: Could not parse input from 'Query File' (but other functions went through with the same query file)

3.       WARNING: Could not parse ref.fasta (but other functions went through with the same reference file)

4.       gnuplot: unable to open display ''  gnuplot: X11 aborted. WARNING: Unable to query clipboard with xclip  -- INTERACTIVE MODE --

Any help is appreciated. Thanks a lot.


Feng

[MUMmer-help] MUMmer SNP output data help

[<ra...@bi...>]

Hi all,
I have been working with Iontorrent platform. I have sequence of a bacteria which was obtained by denovo assembly on Ion torrent platform. I have to use this data as a reference for calling SNP's across 6 samples. So it would be draft genome vs draft genome. I have used the nucmer snp caller. My questions are:
1) can i use this tool for calling SNP's from data generated from Iontorrent platform?
2) Do i need to align the draft sequences first before going to the SNP calling option?
2) Should i cal SNP's from one sample and then compare it with others or all the sample's data can be combined and called for SNP's? for example can i go with command line 
nucmer --prefix=ref_qry ref.fasta sample1.fasta sample2.fasta sample.3.fasta
3) IS there an option to generate unique SNP's to a particular sample and common variants across all the samples?
Thanks in advance,
 
Ramya.
 

[MUMmer-help] Using mummer -m for multiply files

[Ben O. <bo...@gm...>]

Hello,
I am a computer since student, and I am currently working on a new
bioinformatics project.
One of the problem I must solve in order to proceed with my project is the
follow:

"Given m sets of strings (N1, .., Nm) - find all the maximal m-shared
substrings" - I will explain:
(1) substrings that appear at least once in *each *set.
(2) with length greater than "l" that cannot be extended without breaking
(1).
(3) we must be able to attribute each such substring to all its occurrences
in all the subsets.

So I am thinking that the -mum command is the right start for me.
Since the first two bullets actually mean that I want to find MUM (right?)
with minimum length of l.
*But, *as you can see in bullet (1) - I want only MUMs that are shared at
least once in *each *string.
As I understood, if I use the -mum command with N1 as the reference and N2,
N3,...Nm as the queries - it will output the shared MUM between N1 and N2,
and the shared MUM between N1 and N3 and..... and  the shared MUM between
N1 and Nm.
This is not what I want!

Can you please help to figure out what to do?
Thanks a lot!
Ben

Re: [MUMmer-help] problem with mapview

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

Hi Ping,
Sorry, the developer of mapview has moved on and that tool is no longer
supported.

-Adam


On Thu, Jun 4, 2015 at 1:22 PM, Ping Hu <ph...@lb...> wrote:

> Dear MUMMER help,
>
> I installed MUMER3.23 in my user directory install had now error. I have
> an issue with mapview.
> It supposed to have -f with option to generate pdf, .fig or .ps but the -f
> options doesn't work. I can generate .fig file (not sure how to see it) but
> not .pdf or ps.
>
> How do I make the -f option work?
>
> Thanks.
>
> Ping
>
> --
> Ping Hu, Ph.D
> Lawrence Berkeley National Lab
> 510-486-5908
> ph...@lb...
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] problem with mapview

[Ping Hu <ph...@lb...>]

Dear MUMMER help,

I installed MUMER3.23 in my user directory install had now error. I have an
issue with mapview.
It supposed to have -f with option to generate pdf, .fig or .ps but the -f
options doesn't work. I can generate .fig file (not sure how to see it) but
not .pdf or ps.

How do I make the -f option work?

Thanks.

Ping

-- 
Ping Hu, Ph.D
Lawrence Berkeley National Lab
510-486-5908
ph...@lb...

Re: [MUMmer-help] Problem with mummerplot

[Guannan <wan...@gm...>]

Thanks, Adam. I am just not sure whether a 71 GB delta is normal or
not.Most the delta files generated from others in my lab are just in MB
even the alignment between two entire genomes. I will try this again and
monitor the memory usage this time.
Thank you.

Guannan

On Thu, May 28, 2015 at 3:34 PM, Adam Phillippy <aph...@gm...>
wrote:

> Hm, yes, that could be because delta-filter is using too much memory. I'd
> suggest monitoring the memory usage. Also, some managed servers might be
> configured to kill a process using more than some pre allocated amount of
> memory.
>
> Best,
> -Adam
>
>
> On Thu, May 28, 2015 at 3:07 PM, Guannan <wan...@gm...>
> wrote:
>
>> Thanks, Adam. That does make sense. I am ssh'ing to a server where
>> graphical interface is not allowed. I am now running mummerplot with '-t
>> png' to see whether it is working or not. Another problem I have here is
>> that even when I tried delta-filter which doesn't require X, I still ended
>> up with "killed" without any error message. So I even don't know what is
>> the problem here. Do you have any idea about it? Is it because the
>> generated 71GB delta file is too big?
>> Thanks
>>
>> Nan
>>
>> On Thu, May 28, 2015 at 10:16 AM, Adam Phillippy <aph...@gm...>
>> wrote:
>>
>>> This is probably because you don't have a running X server. Mummerplot,
>>> by default, will try and launch an interactive gnuplot window which
>>> requires X. If you don't have X, you can generate a static plot with
>>> mummerplot '-t png' which will generate a png image. (If you are ssh'ing to
>>> a server, and that's what is confusing things, make sure to ssh with the -X
>>> option to forward X)
>>>
>>> Best,
>>> -Adam
>>>
>>>
>>> On Tue, May 26, 2015 at 7:57 PM, Guannan <wan...@gm...>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I have been using Amoscmp-shortreads for a reference-guided assembly,
>>>> in which nucmer is used.
>>>> The command in that pipeline is : /usr/local/bin/nucmer --maxmatch
>>>> --prefix=my_file -l 20 -c 20 my_file.1con my_file.seq.After this, a 71G
>>>> delta file is generated.
>>>> But when I wanted to visualize this delta file with mummerplot, it
>>>> shown 'killed' without any error message. Here is the command I
>>>> used: mummerplot my_file.delta.
>>>> What is the problem here and how should I solve it?
>>>> Thank you.
>>>>
>>>> Nan
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> MUMmer-help mailing list
>>>> MUM...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>>>
>>>>
>>>
>>
>

Re: [MUMmer-help] Problem with mummerplot

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

Hm, yes, that could be because delta-filter is using too much memory. I'd
suggest monitoring the memory usage. Also, some managed servers might be
configured to kill a process using more than some pre allocated amount of
memory.

Best,
-Adam


On Thu, May 28, 2015 at 3:07 PM, Guannan <wan...@gm...> wrote:

> Thanks, Adam. That does make sense. I am ssh'ing to a server where
> graphical interface is not allowed. I am now running mummerplot with '-t
> png' to see whether it is working or not. Another problem I have here is
> that even when I tried delta-filter which doesn't require X, I still ended
> up with "killed" without any error message. So I even don't know what is
> the problem here. Do you have any idea about it? Is it because the
> generated 71GB delta file is too big?
> Thanks
>
> Nan
>
> On Thu, May 28, 2015 at 10:16 AM, Adam Phillippy <aph...@gm...>
> wrote:
>
>> This is probably because you don't have a running X server. Mummerplot,
>> by default, will try and launch an interactive gnuplot window which
>> requires X. If you don't have X, you can generate a static plot with
>> mummerplot '-t png' which will generate a png image. (If you are ssh'ing to
>> a server, and that's what is confusing things, make sure to ssh with the -X
>> option to forward X)
>>
>> Best,
>> -Adam
>>
>>
>> On Tue, May 26, 2015 at 7:57 PM, Guannan <wan...@gm...>
>> wrote:
>>
>>> Hello,
>>>
>>> I have been using Amoscmp-shortreads for a reference-guided assembly, in
>>> which nucmer is used.
>>> The command in that pipeline is : /usr/local/bin/nucmer --maxmatch
>>> --prefix=my_file -l 20 -c 20 my_file.1con my_file.seq.After this, a 71G
>>> delta file is generated.
>>> But when I wanted to visualize this delta file with mummerplot, it shown
>>> 'killed' without any error message. Here is the command I used: mummerplot
>>> my_file.delta.
>>> What is the problem here and how should I solve it?
>>> Thank you.
>>>
>>> Nan
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> MUMmer-help mailing list
>>> MUM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>>
>>>
>>
>

Re: [MUMmer-help] Problem with mummerplot

[Guannan <wan...@gm...>]

Thanks, Adam. That does make sense. I am ssh'ing to a server where
graphical interface is not allowed. I am now running mummerplot with '-t
png' to see whether it is working or not. Another problem I have here is
that even when I tried delta-filter which doesn't require X, I still ended
up with "killed" without any error message. So I even don't know what is
the problem here. Do you have any idea about it? Is it because the
generated 71GB delta file is too big?
Thanks

Nan

On Thu, May 28, 2015 at 10:16 AM, Adam Phillippy <aph...@gm...>
wrote:

> This is probably because you don't have a running X server. Mummerplot, by
> default, will try and launch an interactive gnuplot window which requires
> X. If you don't have X, you can generate a static plot with mummerplot '-t
> png' which will generate a png image. (If you are ssh'ing to a server, and
> that's what is confusing things, make sure to ssh with the -X option to
> forward X)
>
> Best,
> -Adam
>
>
> On Tue, May 26, 2015 at 7:57 PM, Guannan <wan...@gm...>
> wrote:
>
>> Hello,
>>
>> I have been using Amoscmp-shortreads for a reference-guided assembly, in
>> which nucmer is used.
>> The command in that pipeline is : /usr/local/bin/nucmer --maxmatch
>> --prefix=my_file -l 20 -c 20 my_file.1con my_file.seq.After this, a 71G
>> delta file is generated.
>> But when I wanted to visualize this delta file with mummerplot, it shown
>> 'killed' without any error message. Here is the command I used: mummerplot
>> my_file.delta.
>> What is the problem here and how should I solve it?
>> Thank you.
>>
>> Nan
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li...
>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>>
>

Re: [MUMmer-help] Problem with mummerplot

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

This is probably because you don't have a running X server. Mummerplot, by
default, will try and launch an interactive gnuplot window which requires
X. If you don't have X, you can generate a static plot with mummerplot '-t
png' which will generate a png image. (If you are ssh'ing to a server, and
that's what is confusing things, make sure to ssh with the -X option to
forward X)

Best,
-Adam


On Tue, May 26, 2015 at 7:57 PM, Guannan <wan...@gm...> wrote:

> Hello,
>
> I have been using Amoscmp-shortreads for a reference-guided assembly, in
> which nucmer is used.
> The command in that pipeline is : /usr/local/bin/nucmer --maxmatch
> --prefix=my_file -l 20 -c 20 my_file.1con my_file.seq.After this, a 71G
> delta file is generated.
> But when I wanted to visualize this delta file with mummerplot, it shown
> 'killed' without any error message. Here is the command I used: mummerplot
> my_file.delta.
> What is the problem here and how should I solve it?
> Thank you.
>
> Nan
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] Problem with mummerplot

[Guannan <wan...@gm...>]

Hello,

I have been using Amoscmp-shortreads for a reference-guided assembly, in
which nucmer is used.
The command in that pipeline is : /usr/local/bin/nucmer --maxmatch
--prefix=my_file -l 20 -c 20 my_file.1con my_file.seq.After this, a 71G
delta file is generated.
But when I wanted to visualize this delta file with mummerplot, it shown
'killed' without any error message. Here is the command I used: mummerplot
my_file.delta.
What is the problem here and how should I solve it?
Thank you.

Nan