Issues about 'quast-download-busco'

[Carris0819]

Hello genius people, I am trying to download busco and quast in my mamba environment, but I have found that there are few error messgaes came through after the last command line of 'quast-download-busco'.

This is how the error messgaes looks like:
ERROR! Failed downloading bacteria database (url: https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 404: Not Found
You can try to download the file manually, place it in /data/home/carris/miniforge3/envs/sequence_analysis/lib/python3.10/site-packages/quast_libs/busco/bacteria.tar.gz and restart QUAST
WARNING: Failed to download bacteria database from https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gz and unpack it into /data/home/carris/miniforge3/envs/sequence_analysis/lib/python3.10/site-packages/quast_libs/busco
Downloading BUSCO database...
Downloading eukaryota database (file: eukaryota.tar.gz)...

Does anyone know how to solve this problem? Thank you so much for your help!

[alexeigurevich]

Hello,
It seems that old BUSCO databases are (currently?) unavailable from the https://busco-archive.ezlab.org website, so Quast cannot download and configure them. We plan to switch to the latest BUSCO (v.5) in future Quast releases but the work on Quast is not active nowadays (due to other projects for core developers), so I cannot promise you realistic estimates.
Note that Quast can work without BUSCO, just a few corresponding quality metrics will be missing. At the same time, you can obtain the latest BUSCO stats using their tool directly: https://busco.ezlab.org/

[mkweskin]

The busco v3 website is available on the Wayback Machine: https://web.archive.org/web/20230606120407/https://busco-archive.ezlab.org/v3/

A few of the v9 DBs were archived and downloadable:

https://web.archive.org/web/20230330151146/https://busco-archive.ezlab.org/v3/datasets/eukaryota_odb9.tar.gz
https://web.archive.org/web/20221227111026/https://busco-archive.ezlab.org/v3/datasets/insecta_odb9.tar.gz
https://web.archive.org/web/20230330143823/https://busco-archive.ezlab.org/v3/datasets/euarchontoglires_odb9.tar.gz

[pdimens]

Has there been any movement on this? The new paths for the most updated databases are:

https://busco-data.ezlab.org/v5/data/lineages/

e.g.

https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2024-01-08.tar.gz

Alternatively, QUAST could use BUSCO itself to download the datatbase in a [presumably] futureproof way:

busco --download eukaryota_odb10

[pmenzel]

I tried putting the file https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz into the expected location for Quast (when installed via conda this would be: $CONDA_PREFIX/lib/pythonX.X/site-packages/quast_libs/busco/bacteria.tar.gz), and it does not try to download the file, but fails to use it with this message

****************** Start a BUSCO 3.0.2 analysis, current time: 11/18/2024 15:53:35 ******************
Configuration loaded from /home/ptr/temp/quast/busco_stats/config.ini
Init tools...
Check dependencies...
The dataset you provided lacks elements in /opt/conda/miniconda3/envs/xxxxxxx/lib/python3.8/site-packages/quast_libs/busco/bacteria/prfl
BUSCO analysis failed !
Check the logs, read the user guide, if you still need technical support, then please contact mailto:[email protected]

My guess is, that the older version of BUSCO in Quast cannot use the newer odb10 files.

[alexeigurevich]

Yes indeed, we will update BUSCO to the newest version (and databases) in the next release. The new version is also working on macOS, so the long-standing QUAST statement "BUSCO (Linux only)" will also be gone soon.