barrnap-v0.9 debian package has incomplete database

[thackl]

Dear Torsten,

not sure if this has anything to do with you directly, but I just noticed that the barrnap-v0.9 version packaged for Debian/Ubuntu (installed via apt) is shipped with what appears to be a corrupted database. It lacks for example 23S and 28S models (see below). Any idea why that is, how to fix it or where to better report it?

Cheers Thomas

#cd /usr/share/barrnap/db
grep NAME *.hmm
arc.hmm:NAME  16S_rRNA
arc.hmm:NAME  5S_rRNA
arc.hmm:NAME  5_8S_rRNA
bac.hmm:NAME  16S_rRNA
bac.hmm:NAME  5S_rRNA
euk.hmm:NAME  18S_rRNA
euk.hmm:NAME  5S_rRNA
euk.hmm:NAME  5_8S_rRNA
mito.hmm:NAME  12S_rRNA
mito.hmm:NAME  16S_rRNA

[mr-c]

Hello @thackl from Debian; I just saw your report. The normal way to tell the Debian maintainers that there is a problem is to run the reportbug command.

The reason we don't include the 23S and 28S models is due to licensing issues.

However, I see that since release 138 of SILVA (dated 2020-11-03), its

databases, its taxonomy, and all files provided for download are licensed [under the] Create Commons Attribution 4.0 (CC-BY 4.0) [license].

So if we can re-generate these hmms using the new SILVA release, then Debian can include the full set of models.

[mr-c]

@thackl or anyone else willing to test, here is an updated database for barnnap built using the latest RFAM & SILVA releases: barrnap_db_rfam14-9_silva138-1.zip

These pass the make test bigtest tests, but I don't know if other testing is also needed.