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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On Wed, Jun 12, 2013 at 3:06 PM, Berner, Thomas <thomas.berner@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). Thanks, Peter