ports/128271: biology/ncbi-toolkit - blastall segfaults when output is set to XML (-m 7)

Julien Cigar jcigar at ulb.ac.be
Fri Oct 24 14:00:11 UTC 2008


The following reply was made to PR ports/128271; it has been noted by GNATS.

From: Julien Cigar <jcigar at ulb.ac.be>
To: Fernan Aguero <fernan at iib.unsam.edu.ar>
Cc: bug-followup at freebsd.org
Subject: Re: ports/128271: biology/ncbi-toolkit - blastall segfaults when
	output is set to XML (-m 7)
Date: Fri, 24 Oct 2008 15:29:38 +0200

 Hi Fernan,
 
 Thanks for your quick answer.
 I tried the three ways, but neither of them works here :
 
 jcigar at bccm-it blast % cat ~/seq.txt 
 CGAATCGTAACCGTTCGTACGAGAATCGCTGTCCTCTCCTTC%                  
 
 jcigar at bccm-it blast % blastall -i ~/seq.txt -d rodentia.fasta -p blastn
 -m 7
 zsh: segmentation fault  blastall -i ~/seq.txt -d rodentia.fasta -p
 blastn -m 7
 
 jcigar at bccm-it blast % echo "CGAATCGTAACCGTTCGTACGAGAATCGCTGTCCTCTCCTTC"
 | blastall -d rodentia.fasta -p blastn -m 7
 zsh: done                echo
 "CGAATCGTAACCGTTCGTACGAGAATCGCTGTCCTCTCCTTC" | 
 zsh: segmentation fault  blastall -d rodentia.fasta -p blastn -m 7
 
 jcigar at bccm-it blast % cat ~/foo.txt | blastall -d rodentia.fasta -p
 blastn -m 7                      
 zsh: done                cat ~/foo.txt | 
 zsh: segmentation fault  blastall -d rodentia.fasta -p blastn -m 7
 
 I confirm too that it works perfectly with the latest version of the
 ncbi tools.
 
 Thanks
 
 Regards,
 Julien
 
 On Fri, 2008-10-24 at 10:04 -0200, Fernan Aguero wrote:
 > Julie,
 > 
 > I can confirm this bug with blastall 2.2.14 (see attached typescript).
 > I have just updated the ncbi-toolkit port to the latest version (blast
 > 2.2.18) in my box and I can no longer reproduce it, so I understand
 > the bug seems has been fixed.
 > 
 > I will try to submit the update as soon as possible, but it may take
 > some days, as I'm flooded with work right now.
 > 
 > In the meantime, please notice that the segfault when requesting XML
 > format does not occur in all cases (i.e. if XML is what you need you
 > probably don't need to wait for the updated port).
 > 
 > fetch ftp://ftp.ncbi.nih.gov/blast/db/FASTA/vector.gz
 > gzip -d vector.gz
 > formatdb -i vector.gz -p F
 > echo "CGAATCGTAACCGTTCGTACGAGAATCGCTGTCCTCTCCTTC" > test.fna
 > 
 > Three ways of doing the same thing:
 > i) blastall -p blastn -d vector -i test.fna -m7
 > vs
 > ii) echo "CGAATCGTAACCGTTCGTACGAGAATCGCTGTCCTCTCCTTC" | blastall -p
 > blastn -d vector -m7
 > vs
 > iii) cat test.fna | blastall -p blastn -d vector -m7
 > 
 > In my hands (see attached typescript) I can only reproduce the bug
 > when calling blastall as in (ii). I have never been able to get a core
 > dump when calling blastall as in (i) or (iii).
 > 
 > Cheers,
 > 
 -- 
 Julien Cigar
 Belgian Biodiversity Platform
 http://www.biodiversity.be
 Université Libre de Bruxelles (ULB)
 Campus de la Plaine CP 257
 Bâtiment NO, Bureau 4 N4 115C (Niveau 4)
 Boulevard du Triomphe, entrée ULB 2
 B-1050 Bruxelles
 Mail: jcigar at ulb.ac.be
 @biobel: http://biobel.biodiversity.be/person/show/471
 Tel : 02 650 57 52
 



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