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

Fields, Christopher J cjfields at illinois.edu
Thu Nov 10 09:00:46 EST 2011


On Nov 10, 2011, at 7:09 AM, Peter wrote:

> 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

Yeah, that's bad.  I have seen a few things like this myself that make me worry about the transition to BLAST+.

chris

PS - Odd I didn't see this one, was it caught in the bioperl-announce filter?




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