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
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
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