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blastn staxids returning N/A

Every time I try to run Blastn with 'staxids' specified in the outfmt section, I only get a file full of 'N/A's on ever line! Can someone please explain how they have been able to extracts Taxids when using blastn? I've already downloaded taxbd and exported the BLASTDB variable containing the path to me Taxonomic database. here is an example of how I've used the command:

blastn -db /nt -query test.fa -out test.results -outfmt '6 staxids' -perc_identity 90 -max_target_seqs 1
blast
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updated by cpantony • cpantony • written by sharde2 • sharde2

I got the same problem ..

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written by Picasa Picasa

Please use ADD COMMENT, this is not an answer.

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written by Michael Dondrup Michael Dondrup

I have done the same and it works as expected. You are possibly not using the database you want to use. Which version of nt database and blast are you really using?

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written by Michael Dondrup Michael Dondrup

I am using the nt database downloaded from the ncbi site (downloaded using update_blastdb.pl) and my blast version is 2.5.0 x64-linux.

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written by sharde2 • sharde2

1 answer

Hi

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/update_blastdb.pl taxdb
/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/
/home/tools/ncbi-blast-2.3.0+/bin/unzip gi_taxid_nucl.zip

Added the following line to my .bashrc and sourced it:

export BLASTDB='/home/tools/ncbi-blast-2.3.0+/bin'

Also, made a new file .ncbirc with the following content

[BLAST]

BLASTDB=/home/tools/ncbi-blast-2.3.0+/bin

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!

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updated by h.mon h.mon • written by cpantony • cpantony

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