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 > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/