On Wed, Apr 24, 2013 at 11:40 PM, Ganote, Carrie L <cganote@iu.edu> wrote:
Hi list,
I have a newly installed Galaxy instance (security_2013.04.08) and I am testing out NCBI Blast+ on it. I'm having trouble getting it to run.
I'm using the following tools from the Galaxy Main Toolshed: blast_datatypes b3a3ba0c1d47 ncbi_blast_plus 1f546099212f
Those are the latest releases on the main ToolShed, which is good. http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes Revision: 5:b3a3ba0c1d47 Version 0.0.15 http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus Revision: 8:1f546099212f Version 0.0.17 How did you install them? Via the automated Tool Shed install, or manually? How did you setup the databases?
Looks like blast is being called fine, but I get this:
Fatal error: Matched on Error: Error: NCBI C++ Exception:
"/N/soft/rhel6/ncbi-blast+/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
Searching for that error suggests it can be triggered by a bad database: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962 If this is an NCBI database, check the MD5 checksums and/or redownload it. If this is your own database, try deleting it and rebuilding it from the FASTA file.
WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'asn1': 'module' object has no attribute 'GenericAsn1' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'asn1-binary': 'module' object has no attribute 'GenericAsn1Binary'
Anyone seen this?
I think this might be a fault in Galaxy with some recently added ASN1 formats (which we will later be subclassing for using with BLAST or other NCBI tools). The commit was here: https://bitbucket.org/galaxy/galaxy-central/commits/d6f866cbf12d0242089fbbbf... https://bitbucket.org/galaxy/galaxy-dist/commits/d6f866cbf12d0242089fbbbfb79... Curious, Peter