Species level taxID

Question

[danvoronov]

Hi,

I am trying to extract the sequences from the NCBI nt blast database. For this the blastdbcmd needs the species level taxIDs and it tells me to use get_species_taxids.sh. So that's what I did. Since I wanted all the bacterial sequences I used 2 as the highest taxID and thought that the following command would give me only bacterial species IDs

get_species_taxids.sh -t 2 > bactarial_taxIDs.txt

However, I have also order and genus IDs along with the species IDs so the following command does not work.

blastdbcmd -db ncbi_nt_db -dbtype nucl -taxidlist bacterial_taxIDs.txt -out bacteria.fa -outfmt "%f"

Error: [blastdbcmd] Taxonomy ID(s) not found. This could be because the ID(s) provided are not at or below the species level. Please use get_species_taxids.sh to get taxids for nodes higher than species (see https://www.ncbi.nlm.nih.gov/books/NBK546209/).

Is there a way to keep only species level IDs? Thanks.

Danil

[GenoMax]

get_species_taxids.sh to get taxids for nodes higher than species

So that script is not useful for your purposes then.

Is there a way to keep only species level IDs?

[danvoronov]

So "higher" means genus and so on in this case?

[GenoMax]

I grabbed a random set of taxID from get_species command and was able to run the blastdbcmd.

$ more bact.txt 
1206589
1206590
1206591
1206592
1206642
1206643
1206644
1206645
1206646
1206647
1206648

 $ blastdbcmd -db nt -outfmt %f -taxidlist bact.txt | grep ">" 
>JX050253.1 Xanthomonas sp. 6 16S ribosomal RNA gene, partial sequence
>JX050254.1 Pseudomonas sp. 25 16S ribosomal RNA gene, partial sequence
>JX050261.1 Pseudomonas sp. 15 16S ribosomal RNA gene, partial sequence
>JX273662.1 Actinophytocola sp. I10A-01801 16S ribosomal RNA gene, partial sequence
>JX273665.1 Friedmanniella sp. I10A-01803 16S ribosomal RNA gene, partial sequence >JX273666.1 Friedmanniella sp. I10A-01996 16S ribosomal RNA gene, partial sequence
>JX273667.1 Frigoribacterium sp. I10A-01966 16S ribosomal RNA gene, partial sequence
>JX273670.1 Herbiconiux sp. I10A-01569 16S ribosomal RNA gene, partial sequence
>JX273678.1 Algoriphagus sp. I10B-02282 16S ribosomal RNA gene, partial sequence
>JX273680.1 Friedmanniella sp. I10A-01568 16S ribosomal RNA gene, partial sequence
>JX273681.1 Asanoa sp. I10A-01877 16S ribosomal RNA gene, partial sequence
>JX273682.1 Flavobacterium sp. I10A-02067 16S ribosomal RNA gene, partial sequence
>HE962099.1 Enterococcus sp. BGTRS1-35 partial 16S rRNA gene, strain BGTRS1-35

Do you have the taxonomy files available in the same directory where you have your nt index files?