NCBI taxids not matching

Open padpadpadpad opened this issue 4 years ago • 2 comments

Firstly I have found the documentation and usage of mmseqs2 for taxonomic assignment to be extremely good and easy to follow!

However, just a quick point that some of the ncbi taxids given do not match the LCA scientific name.

Below is the output from createtsv from some of my assignments. From previous sequencing I am pretty sure the LCA scientific name (taxa here) is correct, but the ncbi taxa ID do not link to the correct name. For example, there is no tax id for 19759 according to my search here.

tax_id	taxonomic_level	taxa	tax_id_all
58962	species	Achromobacter veterisilvae	2;3;4;46;62;468;58962
2	superkingdom	Bacteria	2
6620	species	Ochrobactrum B soli	2;3;79;91;92;6619;6620
92	family	Rhizobiaceae A	2;3;79;91;92
76	genus	Pseudomonas E	2;3;4;29;30;76
180	genus	Stenotrophomonas	2;3;4;127;128;180
19759	species	Variovorax sp003019815	2;3;4;46;62;2887;19759

Aug 17 '21 09:08 padpadpadpad

I met the same question, taxid:3177 taxon_name: species Ruminococcus E sp003526955 3177 can't found in the NCBI taxonomy databse. @milot-mirdita

Mar 07 '22 07:03 zhou-sumei