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barrnap-v0.9 debian package has incomplete database
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
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.
@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.