On Wed, Jun 12, 2013 at 3:06 PM, Berner, Thomas
<thomas.ber...@jki.bund.de> 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”?
> 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 Gianmauro and Björn for your comments.

There are two issues here, one that we would like to be able to
handle multi-threading better via Galaxy configuration on a
per-tool level, but for now it must often be hard coded or
done via tool-specific environment variables.

Here however, the only reason to change the threads is to
avoid an apparent bug in BLAST itself. The key questions
are how was BLAST installed - if from the tool shed which
one (test of main) and which revision (version).



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