Installation docs need to specify correct version of GTDB to download (max R214)

[smdabdoub]

Since Aviary installs GTDB-tk v2.3.2, users can download, at most, GTDB R214.

GTDB-tk v2.4.0 switches from fastani to skani which changes paths in the database causing the GTDB task in Aviary to fail with the following message:

ERROR: Reference genome missing from FastANI database: release220/fastani/database/GCF...

[smdabdoub]

Manually updating the internal GTDB-tk conda environment to v2.4.0 does not appear to cause any issues.

[julianzaugg]

@rhysnewell Just adding to this: GTDB R220 has now been released, so the documentation (and corresponding GTDB-Tk version 2.4.0) should be updated to reflect this.

[wwood]

Relatedly, the path here:

aviary/aviary/modules/annotation/annotation.smk

Line 77 in 387ac6d

'DB_URL="https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz"; '

'DB_URL="https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz"; '

is now wrong, I guess should be https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_package/full_package/gtdbtk_data.tar.gz

but it should also be pinned to the GTDBtk version being used. There are also some places in the documentation that still refer to r207. We should take a more comprehensive approach as updates will come in the future too.

[Anna-MarieSeelen]

Hi I got the same error as @smdabdoub, and manually updated gtdb-tk in the conda environment used for the gtdb-tk rule using conda update gtdbtk. However I still got the same error, because aviary still thinks its using GTDB-tk v2.3.2 for some reason --> see attached log file. Is there something else I need to change for aviary to work with release220 of the GTDB?

Aviary_5436167_stderr.txt
gtdbtk.log

[Anna-MarieSeelen]

Actually I ran aviary recover again to double check and now the correct version of GTDB-tk, namely 2.4.0. is correctly stated in log file and the GTDB-tk step is thus running for me without errors.