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 ------------------------------------------------------------------------------ AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on "Lean Startup Secrets Revealed." This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users