ncbi blastn database error

[jmartin]

I have an assembly that I want to screen against genbank's NT database. I'm using ncbi blastn v2.6.0+ and I first downloaded the pre-indexed NT from:

ftp.ncbi.nlm.nih.gov/blast/db/nt*.tar.gz

which I extracted and then ran this blastn command:

blastn -db <path>/nt -query <my assembly contigs> -reward 1 -penalty -1 -gapopen 1 -gapextend 2 -word_size 9 -db_soft_mask dust -out <output file> -outfmt 6

and I got an error message saying:

BLAST Database error: Cannot find string algorithm id in algorithm map.


So my first thought was that maybe the pre-packaged version of NT was indexed using a different version of ncbi blast. So then I took the NT fasta file itself and ran:

makeblastdb -in nt -input_type fasta -dbtype nucl -out nt

to index it using the exact version I would be using for the blastn. Then I ran the same blastn command again (pointing to my manually indexed db), and I got the same error message again:

BLAST Database error: Cannot find string algorithm id in algorithm map.


I don't use blast much these days, but in the past I was a heavy user and have never seen this issue before. Can anyone suggest what I'm doing wrong?


Thanks,
John Martin

[r.rosati]

I'm not experienced, but since nobody replied yet: if in `makeblastdb` you chose to name the database "nt", then in `blastn` have you tried using this name, i.e. `-db nt` instead of the complete path? From looking at the code (inexperiencedly) this would seem to be the error:

https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objtools/blast/seqdb_reader/seqdbimpl.cpp

[GenoMax]

@John: I have not seen this error before either. Your original commands should have been fine.

I suggest that you email blast helpdesk with this error. It would be great if you can post their solution in this thread, once you hear back from them.