[Bioperl-l] annot8r_blast2GO

Stefano Ghignone ste.ghi at libero.it
Thu Nov 17 09:10:30 EST 2005

Hi all.
I'm an enthusiast user of annot8r_blast2GO, a sequence annotation script by Ralf Schmid & Mark Blaxter (http://www.nematodes.org/PartiGene/index.html).
The script (that uses the StandAloneBlast) was working fine until I had to upgrade bioperl to 1.5.1 release, to have other scripts working with NCBI.

At the moment I get the following error message for each sequence that I try to parse:

[blastall] WARNING:  [000.000]  seqID: SetUpBlastSearch failed.
[blastall] ERROR:  [000.000]  seqID: BLASTSetUpSearch: Unable to
calculate Karlin-Altschul params, check query sequence.

Regarding this error message, NBCI BLAST Faq says that "This will happen if your entire query sequence has been masked by low complexity filtering", but this is not my case...

Local BLAST installation is working fine; scripts that use StandAloneBlast module are working fine, too (using the same sequence batch I'm trying to annotate).

Is someone experiencing the same problem and/or has a resolution?
Thanks a lot.


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