taxid usage

[phiweger]

How does one specidy the --taxid argument correctly? When I call ...

ncbi-genome-download --taxid 83654 bacteria

... I get ...

ERROR: No downloads matched your filter. Please check your options.

However, this works:

ncbi-genome-download --genus leclercia bacteria

However, I would like to download the entire family, so using the taxid would be much more convenient.

Thank you,
Adrian

[kblin]

The --taxid/--species-taxid parameters are limited to the taxa explicitly mentioned in the assembly summary file from NCBI. --taxid is the ID associated to the exact organism the sequence belongs to, and the other one is the ID of the parent species. No other levels are available for ncbi-genome-download while running because the tool only checks the NCBI FTP server and does not talk to the taxonomy database.

Having said that, @jrjhealey recently contributed an additional script that uses the ETE toolkit to scan through the NCBI taxonomy to find the taxids of all descendant taxa. See https://github.com/kblin/ncbi-genome-download/blob/master/contrib/gimme_taxa.py

That script will create a file with all the taxids that you want to download using ncbi-genome-download.

Hope this helps.