On 06/12/2013 04:06 PM, Berner, Thomas wrote:
>
> Hi guys,
>
>
> another error appeared after we installed NCBI BLAST + to our local
> Galaxy instance and wanted to test it.
>
> After uploading some testdata to our history we tried to run blastn on
> it and got the following error:
>
> Fatal error: Matched on Error:
>
> Error: NCBI C++ Exception:
>
>    
> "/opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
> line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
> Attempt to access NULL pointer.
>
>  
>
> With some testing around we figure out the problem:
>
>  
>
> ./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out
> ~/out2.txt -outfmt "6 std sallseqid score nident positive gaps ppos
> qframe sframe qseq sseq qlen slen" -num_threads 8
>
> Doesn't work until we replaced the "num_threads 8" like it is written
> in the original "ncbi_blastn_wrapper.xml" with "num_threads 1"  
>
> Editing the .xml also solved the problem within the galaxy surface.
>
> Now my question is, is there any other workaround without editing the"
> ncbi_blastn_wrapper.xml"?
>
You can recompile blast+ enabling multithreading (--with-mt option)
-- 
Mauro
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