Quast 5.0.2: BUSCO DBs download fail

[ptrebert]

Hi,
in a fresh Conda environment with only quast=5.0.2, busco=4.0.2 and augustus=3.3.3, running the command quast-download-busco downloads only the Augustus database successfully. The BUSCO databases fail with the message "HTTP Error 301: Moved Permanently", which seems to be a known/re-occurring problem (see #65). A simple wget call with the given URL works fine, and shows that the domain changed from busco.ezlab.org/ to busco-archive.ezlab.org.

Apart from the above, it would be helpful if quast-download-busco would exit with a non-zero code if the database download fails; this would simplify unsupervised and automatic environment setups.

Best,
Peter

[javijevi]

I have the same error. I'd say that it's due to QUAST trying to download the odb9 version of the BUSCO database, whereas I think the BUSCO guys have upgraded to odb10 and eliminated the odb9 links which QUAST tries (e.g., https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz).

Any workaround to this?

Cheers,
Javier.

[alexeigurevich]

The workaround is to use the latest pre-release Quast 5.1.0rc1 -- the BUSCO issue is fixed there. As soon as we will release a mature version 5.1.0, we will add it to conda as well.

[splaisan]

quast 5.0.2

Hi,
I have the same while installing metaWrap and do not dare to upgrade busco risking to break metawrap.
if @ptrebert is right, would it please be possible to change the code of quast-download-busco to point to the right URL.
I see that the url in not hardcoded in that script and do not know where to edit myself.
thanks in advance

I find these potential locations with grep

/opt/miniconda3/envs/metawrap/opt/quast-5.0.2 $ grep -Rwn . -e 'busco.ezlab.org'

Binary file ./quast_libs/run_busco.pyc matches
./quast_libs/busco/busco.py:13:And visit our website `<http://busco.ezlab.org/>`_
./quast_libs/busco/busco.py:81:             'Visit http://busco.ezlab.org for available lineages.')
Binary file ./quast_libs/busco/busco.pyc matches
./quast_libs/run_busco.py:25:bacteria_db_url = 'https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz'
./quast_libs/run_busco.py:26:fungi_db_url = 'https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz'
./quast_libs/run_busco.py:27:eukaryota_db_url = 'https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz'

[splaisan]

quast 5.0.2

OK, it was easy after all!
I edited the three lines in of run_busco.py in my quast conda env and replaced busco.ezlab.org by busco-archive.ezlab.org after what the command quast-download-busco ran perfectly
(thanks @ptrebert for the hint!)