Hi Thomas,

which wrapper did you use, the one from the toolshed or testtoolshed?

Can you have a look at that thread please?
http://dev.list.galaxyproject.org/Blast-Errors-td4659419.html



> 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”?

Not yet, the infrastructure is still missing for such a feature, afaik.
Sorry.

Cheers,
Björn

> Searching in the documentation and the mailing list, I did not find
> anything about this.
> 
> We believe this could be of common interest. It would be great if
> anybody could comment on this.  
> 
> 
> Thanks a lot, Thomas
> 
>  
> 
> 
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