the program is blastn -task blastn-short -query rfam_trimed_short_uniq.fa -db /root/bio-analysis-soft/database/gss-est-db/tage -ungapped -penalty -1 -reward 1 -outfmt 6 -out 2 -num_threads 12
I get an error.Error: NCBI C++ Exception:
"/root/bio-analysis-soft/msw/ncbi-blast-2.2.27+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
I think the error caused by -num_threads 12.can you help me ?
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2011101101 •
I guest you compiled your BLAST+ from source tarball.
To use num_threads, you have to add a "--with-mt" argument when run configre to support multithreads.
You can follow this manual: BLAST Command Line Applications User Manual
cd c++
./configure --without-debug --with-strip --with-mt --with-build-root=ReleaseMT
cd ReleaseMT/build
make all_r
Installing BLAST+ executables is the better choice. Compilation from source costs long time and errors may occur.
Not when they have got the "wrong" compile options. Also if that you claim is true then the Gentoo distribution is a bad idea is general (spoiler: it is not).
According to NCBI's BLAST Manual:
num_threads integer 1 Number of threads (CPUs) to use in blast search.
The command-line option is mostly referred to using CPUs (as opposed to simple threads) in the manual. I suspect you don't have 12, but did you try it with the number of CPUs you actually have got?
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Michael Schubert
My ,cups 4 ,but 16 core.when num_threads 2,there is still an error
I think whenever I've seen that error, the query fasta file has had problems: can you check for
On a side note - I seem to remember seeing a tool that checks and cleans Fasta files... might be worth running once on your query file
when num_threads 1,there is no error
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