SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
error with sam output ->Parse error at line xxxxx: missing colon in auxiliary data manore Bioinformatics 11 11-25-2013 01:50 PM
error in picard (SAM validation error) dongshenglulv Bioinformatics 3 07-05-2013 12:58 PM
Tophat Error: Error: segment-based junction search failed with err =-6 sjnewhouse RNA Sequencing 8 03-19-2013 04:14 AM
tophat2 segment_juncs error: Error: segment-based junction search failed with err =-6 hulan0@gmail.com Bioinformatics 1 04-16-2012 06:37 AM
help needed with Bambus error..grommit error roshanbernard Bioinformatics 0 03-17-2011 07:41 PM

Reply
 
Thread Tools
Old 06-21-2012, 07:17 AM   #1
aleo
Junior Member
 
Location: Barcelona

Join Date: Dec 2011
Posts: 1
Default mummerplot error

Good day,

Help me please with plotting mummer alignment.
I've created out.mums file with command
../sparseMEM/mummer -mum -b reference.fa query.fa >out.mums.
Both input fasta file are multi-fasta sequences, ~9.000 of records in each. Actually it is a draft assemblies.
When I am trying to plot it using mummerplot,following the documentation, I always receive an error:

" set ticscale 0 0
^
"mummer.gp", line 13: warning: Deprecated syntax - please use 'set tics scale' keyword
"
Then I've tried to create small test *.mums file with usual mummer command
../mummer-3.22/mummer -mum -b -c testReference.fa testQuery.fa >testOut.mums

But mummerplot could not plot *.mums file, it returns the same error.

When I used nucmer for aligning, it has created *.delta file, and this delta file is plotting perfectly. But for my real files usual mummer and nucmer always crashes with segmentation fault error.

I need to create dot-plot, so what you'll suggest me to do?

Regards,
Vlasova Anna
---------------------------------------------
Bioinformatica i Genomica
CRG-Centre for Genomic Regulation
C/ Dr. Aiguader, 88
Edif. PRBB
08003 Barcelona, Spain
aleo is offline   Reply With Quote
Old 09-04-2012, 09:38 AM   #2
rama
Member
 
Location: Boston, USA

Join Date: Jan 2011
Posts: 20
Default Hi,

I was wondering if you ever got this problem solved. I am now having the same problem and when I searched online found your post. I will be grateful if you can share with me how you resolved this issue or what other alternatives did you find.

Thanks for reading.

Rama
rama is offline   Reply With Quote
Old 07-01-2013, 02:54 AM   #3
pari_89
Member
 
Location: Newcastle upon Tyne

Join Date: Apr 2013
Posts: 55
Default

Quote:
Originally Posted by aleo View Post
Good day,

When I used nucmer for aligning, it has created *.delta file, and this delta file is plotting perfectly. But for my real files usual mummer and nucmer always crashes with segmentation fault error.

I need to create dot-plot, so what you'll suggest me to do?

Regards,
Vlasova Anna
---------------------------------------------
Bioinformatica i Genomica
CRG-Centre for Genomic Regulation
C/ Dr. Aiguader, 88
Edif. PRBB
08003 Barcelona, Spain
Hi, can you please tell me how you plotted the nucmer.delta file using mummer please?? I mean which commands did you use. I am trying to map contigs to a reference sequence.

THank you.
pari_89 is offline   Reply With Quote
Old 08-04-2013, 05:25 AM   #4
louis_ly
Junior Member
 
Location: China

Join Date: Jun 2013
Posts: 4
Default

Hello, everyone.
Today, I followed the case to learn how to use mummer,

In 4.1. Aligning two finished sequences
The most basic use case is the alignment of two contiguous sequences. For all of the one vs. one use cases the mummer program alone, when coupled with mummerplot, may be all that is necessary to visualize a global alignment of the two sequences. This process alone can be very helpful in determining the large scale differences between the two sequences. For a single reference sequence ref.fasta and a single query sequence qry.fasta in FastA format, type:
mummer -mum -b -c ref.fasta qry.fasta > ref_qry.mums

till now, it seems every goes well, a file named ref_qry.mums was generated, but when I try to type the next commend,

mummerplot --postscript --prefix=ref_qry ref_qry.mums

an error appeared,
defined(%hash) is deprecated at /usr/bin/mummerplot line 884.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 894.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 981.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 991.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 1034.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 1044.
(Maybe you should just omit the defined()?)
gnuplot 4.4 patchlevel 3
Reading mummer file ref_qry.mums (use mummer -c)
ERROR: Could not parse ref_qry.mums
10003036 5474049 20

what's wrong? Is there anyone can tell me?
louis_ly is offline   Reply With Quote
Old 08-06-2013, 12:56 AM   #5
pari_89
Member
 
Location: Newcastle upon Tyne

Join Date: Apr 2013
Posts: 55
Default

Quote:
Originally Posted by louis_ly View Post
Hello, everyone.
Today, I followed the case to learn how to use mummer,

In 4.1. Aligning two finished sequences
The most basic use case is the alignment of two contiguous sequences. For all of the one vs. one use cases the mummer program alone, when coupled with mummerplot, may be all that is necessary to visualize a global alignment of the two sequences. This process alone can be very helpful in determining the large scale differences between the two sequences. For a single reference sequence ref.fasta and a single query sequence qry.fasta in FastA format, type:
mummer -mum -b -c ref.fasta qry.fasta > ref_qry.mums

till now, it seems every goes well, a file named ref_qry.mums was generated, but when I try to type the next commend,

mummerplot --postscript --prefix=ref_qry ref_qry.mums

an error appeared,
defined(%hash) is deprecated at /usr/bin/mummerplot line 884.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 894.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 981.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 991.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 1034.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 1044.
(Maybe you should just omit the defined()?)
gnuplot 4.4 patchlevel 3
Reading mummer file ref_qry.mums (use mummer -c)
ERROR: Could not parse ref_qry.mums
10003036 5474049 20

what's wrong? Is there anyone can tell me?
Hi there, I think you are running the command wrongly. The command in the documentation says this :

mummerplot -x "[0,275287]" -y "[0,265111]" -postscript -p mummer mummer.mums

-x and - y are the coordinates for the dot plots, then use mummer for the .mums file and not prefix.

I hope this helps
pari_89 is offline   Reply With Quote
Old 08-07-2013, 02:48 AM   #6
SES
Senior Member
 
Location: Vancouver, BC

Join Date: Mar 2010
Posts: 275
Default

Quote:
Originally Posted by louis_ly View Post
mummerplot --postscript --prefix=ref_qry ref_qry.mums

an error appeared,
defined(%hash) is deprecated at /usr/bin/mummerplot line 884.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 894.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 981.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 991.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 1034.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 1044.
(Maybe you should just omit the defined()?)
gnuplot 4.4 patchlevel 3
Reading mummer file ref_qry.mums (use mummer -c)
ERROR: Could not parse ref_qry.mums
10003036 5474049 20

what's wrong? Is there anyone can tell me?
There are a couple of things wrong. The first set of messages are just Perl warnings you can safely ignore (I actually fixed this issue with my local version and hopefully someone will fix the source). The last line is the informative part. It says there was an error reading your mums file. This may or may not mean there is something wrong with your mummer output, but your command looks fine. Though, I'm not sure those coordinates look correct. You may want to re-run mummer and try mummerplot again.

You can take at look at the mummerplot examples online and also read the command line documentation for how to call each program. Your mummerplot command looks okay also, so it's likely that something is not right with your mummer file, as the error message would indicate.
SES is offline   Reply With Quote
Old 02-27-2014, 07:12 AM   #7
Beuss
Junior Member
 
Location: Capelle-en-pévèle

Join Date: Feb 2014
Posts: 3
Default

Quote:
mummerplot --postscript --prefix=ref_qry ref_qry.mums

an error appeared,
defined(%hash) is deprecated at /usr/bin/mummerplot line 884.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 894.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 981.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 991.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 1034.
(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /usr/bin/mummerplot line 1044.
(Maybe you should just omit the defined()?)
gnuplot 4.4 patchlevel 3
Reading mummer file ref_qry.mums (use mummer -c)
ERROR: Could not parse ref_qry.mums
10003036 5474049 20
There an error in mummerplot perl script.
You have to correct two regular expression.
in a terminal :
$ vi path/to/mummer/directory/mummerplot
go to line 565
replace :
if ( /^\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {
by :
if ( /^\s*(\d+)\s+(\d+)\s+(\d+)$/ ) {

do it again on line 575

Quick explanation : it search for a line that begin with one or more space, but when you have a start superior to 9999999, this space do not exist anymore.
So if you change '+' by '*' it search for 0 or more spaces.
Beuss is offline   Reply With Quote
Old 02-27-2014, 07:22 AM   #8
SES
Senior Member
 
Location: Vancouver, BC

Join Date: Mar 2010
Posts: 275
Default

Quote:
Originally Posted by Beuss View Post
There an error in mummerplot perl script.
You have to correct two regular expression.
in a terminal :
$ vi path/to/mummer/directory/mummerplot
go to line 565
replace :
if ( /^\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {
by :
if ( /^\s*(\d+)\s+(\d+)\s+(\d+)$/ ) {

do it again on line 575

Quick explanation : it search for a line that begin with one or more space, but when you have a start superior to 9999999, this space do not exist anymore.
So if you change '+' by '*' it search for 0 or more spaces.
Thanks for the information, that is helpful. By the way, those other messages above the error are just warnings that can be ignored. What the message is saying is that the syntax
Code:
if (defined(%hash)) { ... }
is deprecated. It also tells you exactly how to fix the issue and avoid the warnings.

It should be replaced with
Code:
if (%hash) { ... }
That is probably clear though.
SES is offline   Reply With Quote
Old 09-07-2014, 06:40 AM   #9
louis_ly
Junior Member
 
Location: China

Join Date: Jun 2013
Posts: 4
Default

Thank Beuss.

it works!
louis_ly is offline   Reply With Quote
Reply

Tags
alignemnt, dot-plot, mummer

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO