I struggled with this same problem for a few hours or so..Then I did the following (I'm using ncbi-blast-2.3.0+ version):
/home/tools/ncbi-blast-2.3.0+/bin/update_blastdb.pl --decompress nt (This step can take a few hours to complete)
/home/tools/ncbi-blast-2.3.0+/bin/tar -xzf taxdb.tar.gz
#Downloaded gi_taxid_nucl.zip from here ftp://ftp.ncbi.nih.gov/pub/taxonomy/
Added the following line to my .bashrc and sourced it:
Also, made a new file .ncbirc with the following content
I think doing either of the above two steps will work but I did both anyways!
Not sure if this step is necessary in any way (perhaps this is me being superstitious/plain dumb) but I did this too anyways:
Copied taxdb.btd and taxdb.bti from /bin to also where my query fasta file was.
I don't anymore get staxids as N/A while doing blastn. Hope this helps you folks!
modified 10 months ago
h.mon ♦ 27k
2.2 years ago by
cpantony • 10