[KiTrinet]

I tried to follow your directions when maqindex -i -c alignment.cns alignment.map
I obtain
-- Indexing the alignment file 'alignment.map' ... DONE!
-- Indexing the alignment file 'alignment.cns' ... DONE!

than i go on maqview -c alignment.cns alignment.map
freeglut (maview) failed to open display ' '

thanks,

[olus]

maqindex segmentation fault (seqid too large)

Thanks every body for this community.

I had experienced "segmentation fault" with maqindex 2.5 when trying to index .map files (1 solexa lane, 14,853,012 sequences, pair end, 36 bp).
The reference genome is Sc288 (Yeast 12Mbp).

I tried with mapview-2.6, commented out line 11 of const.h, and compiled.
Everithing goes fine

But when I did the following:
$ maqindex -c s_8.consensus.cns -i s_8.map
I had this:
-- Indexing the alignment file 's_8.map' ... -- Found error seqid is too large 1549491744 >= 17 in notify -- maqmap_index.c:123 --
Segmentation fault

Can you help me to interpret this error?

My Best.
G.

[olus]

maqindex segmentation fault (seqid too large)

Thanks every body for this community.

I had experienced "segmentation fault" with maqindex 2.5 when trying to index .map files (1 solexa lane, 14,853,012 sequences, pair end, 36 bp).
The reference genome is Sc288 (Yeast 12Mbp).

I tried with mapview-2.6, commented out line 11 of const.h, and compiled.
Everithing goes fine

But when I did the following:
$ maqindex -c s_8.consensus.cns -i s_8.map
I had this:
-- Indexing the alignment file 's_8.map' ... -- Found error seqid is too large 1549491744 >= 17 in notify -- maqmap_index.c:123 --
Segmentation fault

Can you help me to interpret this error?

My Best.
G.

[Jonathan]

Those *should* be the very steps to success;

For maqview/maqindex to work the cns needs to be binary (afaik),
so... I'm currently out of ideas.

could you paste the exact 'message' from maqindex?

Best
-Jonathan

[KiTrinet]

first, i convert my fasta file into bfa
than convert my fastq file into bfq
after that i obtain the map file using bfa and bfq
maq match alignment.map alignment.bfa alignment.bfq
it has 3 runs at 126% each
than once i obtain that
i use
maq assemble alignment.cns alignment.bfa alignment.map
than it tells me that consensus file has been created and it is in binary format which i cannot view it.
than i try to use maqindex -i -c alignment.cns alignment.map
but it tells me that alignment.cns is failing therefore i need to do mapass2maq for the alignment.cns but it fails giving me an error of the failure of the alignment

i tried multiple ways but i could not obtain any results
thats where i actually stopped
than i tried to use that to view the files in mapview but i still was not able to do anything.

please let me know if you further want me to discuss it i tried to cover step by step, i hope this will allow you to see where i am making a mistake.

thanks,

K

[Jonathan]

Why would you want to convert the binary cns to acgt?

Could you list your maq-steps, that would allow me to better understand
what you are trying to achieve.

Best
-Jonathan

[KiTrinet]

Hi Jonathan

thanks for the information. i tried to follow your direction but unfortunately the cns file is a binary file and i am failing towards converting to acgt.
my maq is the newest version so is the maqview.
After i try to run the data, i obtain this

<3125> 6/9/2009 1:01:06 PM
Element No.4 is not a number! P = t????2???{???mr???.??y^?WyM????)?u?k?N*zi%?QcJ?+f?Z?r?A?????FP?????V?}?4??A46???w??iA????6??]E????f5?@%???|??'g???q?D???V?b????u????q??ik??'G?dP?E???0P3a
<3728> 6/9/2009 1:01:08 PM
Element No.4 is not a number! P = ?U~3?X9?n=???26?A@??$??
<4244> 6/9/2009 1:01:09 PM
Element No.4 is not a number! P = ?
Line: ?)
<4733> 6/9/2009 1:01:11 PM
Element No.4 is not a number! P = ????l?U?1L9?%&??A
Line: ?????.?????:???????n?????x???3FEzPl?#\??|????t???}???????????}\C?,o|~8??t????`?$?J?(O?????H?E?p<?????P?}>?4?0?>=D ?p(
<5132> 6/9/2009 1:05:47 PM
MVFmaker Output: C:\Users\Ahmeti Inc\Desktop\30EFN.6\30EFN_6_30EFN_6.MVF
Total:269,760,457 (A:9,918,429 T:11,513,113 G:13,220,293 C:10,534,443 N:224,574,179)
READS SUM:0 [+]0 [-]0 [contains 'N']0
Mismatch:0 (0) (N:0)
Paired speed: --- MB/s Sort speed: 0.01 MB/s Conversion speed: 5.05 MB/s


can you please let me know what should i do in order to resolve this issue?
If possible please let me know I would be more than happy to share more information, I just dont know how other approach to do.
the entire process fails as i try to create the MVF file. when i go to MVFmaker the process starts it counts how many ATGCN i have but is not able to provide the final sequence.

thanks,

KiTri

[Jonathan]

Perhaps the best approach would be to rerun the alignment with a current MAQ version, and then try maqview with the new cns and new map again;

Otherwise I'd say it's like finding a needle in the haystack to pinpoint your problem!

Best
-Jonathan

[KiTrinet]

error

Hi everyone I have a question in regards to viewing data in maqview,
i obtained a binary file cns in maq however whenever i try to maqindex with map file i fail to do get any information

i will briefly describe the commands

first

i try to convert the old map file into new map file using

maq mapass2maq old.map new.map

than once that gets converted i use

maqindex xxx.cns new.map

however there is a segmentation failure over here

so i tried to carry it at maqview but also failed in this process the files did not convert to mvf

can someone suggest me how to approach using this software

PS if it sounds stupid to anyone i apologize i am new at it,

Regards,

KiTri

[Torst]

GLUT is the OpenGL user toolkit. The glut.h is a C header file for compiling programs which use the toolkit (like MaqView does).

As you are using apt-get I assume you have a Debian or Ubuntu system. If you go to System :: Administration :: Synaptic Packager Manager and search for "GLUT" you will see lots of glut related packages you don't have installed.

To get the glut.h file for compiling software, you will need the correct -dev package. For example, freeglut3-dev and/or libglut3-dev .

Hope that works for you.

[Albert N]

You need to install the "automake" software package as the autogen.sh script needs it.

If automake is not installed, there is a good chance that none of the developer/compilation packages are installed either (eg. gcc) so you may be busy for a while!

hi,
thanks for your reply.
It works perfectly (sudo apt-get install automake)!!!
but now it seems that I don't have the GLUT/glut.h library
As you said, I will be busy for a while

[Torst]

I have some troubles triying to compile maqview-0.2.6
albert@mambara:~/maqview$ ./autogen.sh
running: aclocal
eval: 1: aclocal: not found
error: while running 'aclocal'

You need to install the "automake" software package as the autogen.sh script needs it.

If automake is not installed, there is a good chance that none of the developer/compilation packages are installed either (eg. gcc) so you may be busy for a while!

[Albert N]

Can somebody help a desperate student?

Heeeelp!

I have some troubles triying to compile maqview-0.2.6 (sorry I'm a beginner).
Install file says: "To compile it, just run"./autogen.sh; ./configure; make"......but when I type ./autogen this is the output:
albert@mambara:~/maqview$ ./autogen.sh
running: aclocal
eval: 1: aclocal: not found
error: while running 'aclocal'

Somebody knows what am I doing wrong?

[bosTau2]

//typedef signed long long int int64_t; fixes the problem

Thank you for both answering my questions. I tried both but
//typedef signed long long int int64_t; fixed my problem.

This is a bit different issue but related to a sequence viewer. Have any one tried ssaha_pileup/view_pileup which provide very simple alignments around a single coordinate?

I used MAQ and ssaha2 for a same data set. MAQ and maqview(0.2.5) gave me clean alignments. But ssaha_pileup/view_pileup showed me bad alignments. ssaha2 told me that 97% of the reads are aligned.

I have another question to ruanjue. How difficult is it to convert MAQ alignment format to ace or some alignment format keeping essential information? I am interested in converting ssaha2 alignment format shown below to mapview output for LookSeq (Magnus, Sanger) tools. LookSeq uses MAQ output format. I was told that I should consult with others before I try this.


Score Q_Name S_Name Q_Start Q_End S_Start S_End Direction #Bases identity
95 query subject 1 121 1 120 F 121 95.87 121

Query 1 AACTAAGCTTTCATATCTGCAAGCATCTTTGGGAATACTCTTGACATTGATT 59
v -
Sbjct 1 AACTAAGCTTTCATATCTCCAAGCATCTTTGGGAATACTCTTGACATTGATT 60

Base quality etc are available in different files.

[Torst]

bosTau2,

I had to edit "const.h" and comment out the int64_t typedef, as there was already a "previous declaration" in another .h file it included:

//typedef signed long long int int64_t;

That allowed compilation to succeed on my 64 bit Linux systems.

--Torst