SILVA 138.2 ssu-nr99 database, only 6 levels

[feixiang1209 (Xiang)]

I created the qiime format qza using SILVA-138.1-ssu-nr99 around one year ago, and always used it with no issues. However, yesterday, I downloaded the new 138.2-ssu-nr99 using RESCRIPt, and it now shows an error while using qiime taxa collapse. It seems the new data base has no information of species, only to genus. Could you please advise if there is any changes in the SILVA ssu nr99 data base?

Thanks

Plugin error from taxa:

Requested level of 7 is larger than the maximum level available in taxonomy data (6).

Debug info has been saved to /tmp/qiime2-q2cli-err-yj8xhjz8.log

[SoilRotifer (Mike Robeson)]

Hi @feixiang1209,

SILVA does not curate species level taxonomy. Moving forward we will, honor their intent, and likely no longer include the organism names as the species labels by default, for reasons outlined here, under the "Species-labels: caveat emptor!" drop menu.

You can certainly do this your self by using the --include-species-labels flag during download. Otherwise to make your plots, just set your rank depth as follows:

qiime taxa collapse --p-level 6 ...

Remember if something ever goes wrong always check out the help text first by adding --help to the command.

[feixiang1209 (Xiang)]

@SoilRotifer

SILVA does not curate species level taxonomy. Moving forward we will, honor their intent, and likely no longer include the organism names as the species labels by default, for reasons outlined here, under the "Species-labels: caveat emptor!" drop menu.

Thans a lot. It really helped me out.