Where did you got this message exactly ?

                                                     Sébastien
________________________________________
De : Huanle LIU [elzed...@gmail.com]
Date d'envoi : 15 juillet 2011 03:28
À : Sébastien Boisvert
Objet : Re: RE : RE : [Denovoassembler-users] what does this warning mean?

Hi Sébastien,

I got this after running Ray for a while.

[biol-dortiz02d:04336] *** Process received signal ***
[biol-dortiz02d:04336] Signal: Segmentation fault (11)
[biol-dortiz02d:04336] Signal code:  (0)
[biol-dortiz02d:04336] Failing at address: 0x0
[biol-dortiz02d:04335] *** Process received signal ***
[biol-dortiz02d:04335] Signal: Segmentation fault (11)



Is this a signal of lack of enough computational resource?

Best,

Huanle

On 15/07/2011, at 2:14 PM, Sébastien Boisvert wrote:

OK

                                                    Sébastien
________________________________________
De : Huanle LIU [elzed...@gmail.com]
Date d'envoi : 14 juillet 2011 20:52
À : Sébastien Boisvert
Objet : Re: RE : [Denovoassembler-users] what does this warning mean?

Thanks a lot. Sébastien.

This helps.


On 15/07/2011, at 9:25 AM, Sébastien Boisvert wrote:

In Ray, fastq files must have the extension .fastq.

   Input files

   .fasta
   .fasta.gz (needs HAVE_LIBZ=y at compilation)
   .fasta.bz2 (needs HAVE_LIBBZ2=y at compilation)
   .fastq
   .fastq.gz (needs HAVE_LIBZ=y at compilation)
   .fastq.bz2 (needs HAVE_LIBBZ2=y at compilation)
   .sff (paired reads must be extracted manually)
   .csfasta (color-space reads)

   Note: file format is determined with file extension.


ln -s h.fq h.fastq
ln -s d.fq d.fastq
mpirun -np 2 ./Ray -k 30 -s h.fastq -s d.fastq -o dh




________________________________________
De : Huanle LIU [elzed...@gmail.com]
Date d'envoi : 14 juillet 2011 06:48
À : 
denovoassembler-users@lists.sourceforge.net<mailto:denovoassembler-users@lists.sourceforge.net>
Objet : [Denovoassembler-users] what does this warning mean?

Hi there,

I have installed Ray 1.6.0.

I was able to run those example data sets.

However, when it came to my own data, i always got this warning message:
terminate called after throwing an instance of 'std::out_of_range' what(): 
basic_string::substr

The command line i used is :

mpirun -np 2 ./Ray -k 30 -s h.fq -s d.fq -o dh


Could anyone help me figure out the rub?

Thanks in advance.


Cheers,

Huanle




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