BLASTN Segmentation Fault

Olga Belenkiy olga.belenkiy at weizmann.ac.il
Mon Aug 12 07:22:15 EST 2002


Sometimes the "Segmentation fault (core dumped)" error is the sign that 
the program has run out of memory due to memory limitation of the 
program (in this case unlikely, since BLASTN is build for comparing to 
NT), or of the system on which the program is run (Linux/Unix etc.). On 
Unix you can solve this problem by using the command "unlimit" (check 
the system memory status first using "limit").

Olga.

Kael Fischer wrote:

> Hey all - I have a problem with a fresh build of blast.  The build 
> proceeded without crashing.  The search apparently is completed, and 
> then the seg fault happens just as the results are going to be 
> printed. (the database is 1.5GB current formatted 'nt').  Does anybody 
> know about this one?
>
> (Sorry if this has been covered; a search of the newsgroup only turned 
> up the >2GB problem)
>
> System: FreeBSD 4.6
>
> Command: ./blastall -p blastn -d /usr/local/blast/db/nt -i ~/test.fasta
>
> Output:
> BLASTN 2.2.3 [May-13-2002]
>
>
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs",  Nucleic Acids Res. 25:3389-3402.
>
> Query= gi|21666658|gb|AF441258.1| Mesoplodon perrini TMMC-C75
> mitochondrial control region, partial sequence
>          (433 letters)
>
> Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
> or phase 0, 1 or 2 HTGS sequences)
>            1,357,022 sequences; 6,227,440,795 total letters
>
> Searching...................................................done
>
>                                                                  
> Score    E
> Sequences producing significant alignments:                      
> (bits) Value
>
> Segmentation fault (core dumped)
> ----EOF----
>
> ---
>

-- 

Olga Belenkiy

Molecular Genetics dept.         | olga.belenkiy at weizmann.ac.il
Weizmann Institute of Science,   | fax: ##972 (8) 934 4108
POBox 26, Rehovot 76100, Israel. | tel: ##972 (8) 934 4911
        http://bioinformatics.weizmann.ac.il/~olgab





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