How To Get The Result Which Mismatch 1 To The Query Sequence By Nucleotide-Nucleotide Blast 2.2.27+

Question

[2011101101]

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 ?

Answer 1

[shenwei356]

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

[shenwei356]

Installing BLAST+ executables is the better choice. Compilation from source costs long time and errors may occur.

[Michael Schubert]

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).

Answer 2

[Michael Schubert]

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?

[2011101101]

My ,cups 4 ,but 16 core.when num_threads 2,there is still an error

Answer 3

[Sujai Kumar]

I think whenever I've seen that error, the query fasta file has had problems: can you check for

• blank sequences (i.e. no sequence after a line beginning with ">"); or
• tabs in the fasta header
• non-standard line endings (Win/DOS endings on Linux/OSX etc)

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

[2011101101]

when num_threads 1,there is no error