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bioinformatics-centre / kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
http://kaiju.binf.ku.dk
GNU General Public License v3.0
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Problem with rank Order. #41

Closed davidvilanova closed 7 years ago

davidvilanova commented 7 years ago

Hi , while running kaiju i noticed a problem with Class and order taxonomy. See the following example

C       k141_1685_2     169292  689     169292, WP_049377218.1, TELRRFRSDQGVKPSQKVPGRLDFAAADLAGQEELVRNLANTTAPGEDFDPSASIEVRLSQATVEVTLDTHGAVDVEAERKRLEKDLAKANKELEQTGKKLGNENFLSKAPEEVVNK
IKERQQIAREEVERITSRLEGLK,        Actinobacteria; Corynebacteriales; Actinobacteria; Corynebacteriaceae; Corynebacterium; Corynebacterium aurimucosum;

NCBi taxid 169292 corresponds to : cellular organisms; Bacteria; Terrabacteria group; Actinobacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae; Corynebacterium;Corynebacterium aurimucosum

I´m trying to get "Phylum","Class","Order","Family","Genus","Species" through the command addTaxonNames -t nodes.dmp -n names.dmp -i kaiju_output.ncbi_id -r phylum,order,class,family,genus,species

The rank order based on NCBI is Corynebacteriales but Kaiju returns Actinobacteria

Maybe i´m doing something wrong ?? I have downloaded taxdump.tar.gz as suggested.

pmenzel commented 7 years ago

Yeah, check the command you are running: order and class are switched. I messed that up in the README, but it was fixed in this commit 508406578120a2beef81e70b7e7f0e4ab23d14d0 some time ago.

davidvilanova commented 7 years ago

great , thanks for the update