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