[Bioperl-l] [Bioperl-announce-l] Null Pointer - NCBI C++ Exception

Peter biopython at maubp.freeserve.co.uk
Thu Nov 10 08:09:40 EST 2011


Re: http://lists.open-bio.org/pipermail/bioperl-announce-l/2011-May/000253.html

On Thu, May 19, 2011 at 11:15 PM, rgoldade <rgoldade at sfu.ca> wrote:
>
> I received the following error while trying to run bl2seq from
> standaloneblastplus. Has anyone else encountered this problem?
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: /usr/bin/blastp call crashed: There was a problem running
> /usr/bin/blastp : Error: NCBI C++ Exception:
>
> "/am/ncbiapdata/release/blast/src/2.2.24/Linux32-Suse-icc/c++/ICC1010-ReleaseMT--Linux32-Suse-icc/../src/corelib/ncbiobj.cpp",
> line 688: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to
> access NULL pointer.
>
> Thank you,
> Ryan

Just hit something very very similar, looks like a BLAST+ bug which I
will report now:

$ tblastn -out NC_003197_vs_NC_011294.tsv -outfmt 6 -query
NC_003197.fna -evalue 0.0001 -subject NC_011294.fna
Error: NCBI C++ Exception:
    "/am/ncbiapdata/release/blast/src/2.2.25/IntelMAC-universal/c++/GCC401-ReleaseMT--IntelMAC-universal/../src/corelib/ncbiobj.cpp",
line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
Attempt to access NULL pointer.

This was on a Mac using BLAST 2.2.25+ (tblastn) whereas yours was
BLAST 2.2.24+ (blastp) from the look of the error. The line number has
changed by one, but I'm confident it is the same point of failure.

In my case I was comparing nucleotide against nucleotide, so should
have been using tblastx not tblastn, but it still shouldn't have had a
pointer exception.

Peter


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