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

Peter biopython at maubp.freeserve.co.uk
Thu Nov 10 14:27:22 EST 2011


On Thu, Nov 10, 2011 at 2:00 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> 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

I'm told is already fixed and will be part of BLAST 2.2.26+ which is good.

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

Maybe once, but it was in the archive and my email account.

Peter



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