NCBI taxonomy failing to download

[Vishal Joshi]

HI ete3 team,

I am trying to download NCBITax using ete3 toolkit. Our code is currently failing as the FTP is not reachable.

-----

, in update_db
    (md5_filename, _) = urlretrieve("https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.md5")

...

...

    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 8] nodename nor servname provided, or not known>

------

is there a planned downtime on FTP (https://ftp.ncbi.nih.gov/pub/taxonomy)?

[dengzi...@gmail.com]

Hi,

And yes, we noticed this issue. It turns out the url address for ncbi for taxonomy database has been updated, now new link is https://ftp.ncbi.nlm.nih.gov/pub/taxonomy. The latest url address of ncbi has been updated in our branch https://github.com/etetoolkit/ete/tree/ete3. 

Installing with 

pip install "git+https://github.com/etetoolkit/ete.git@ete3"

or manually change the url address in 

from https://ftp.ncbi.nih.gov/pub/taxonomy to https://ftp.ncbi.nlm.nih.gov/pub/taxonomy in `ete3/ncbi_taxonomy/ncbiquery.py` 

Best,

Ziqi

[Vishal Joshi]

Hi Ziqi,

Thanks for replying. I will try to use the package from the specific branch you mentioned in the last email.

This installation is a part of an automatic procedure which runs every 6 weeks and creates a docker image. Having this pointing to a branch is not a sustainable solution.

Do you have plans to release it soon in master? I wonder there would be other users who would be facing the same issue.

Once it is released, our builds will automatically pick up the latest version

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Cheers,

Vishal Joshi

[ziqi deng]

Hi Vishal,

we have already released in our main branch actually. ETE Toolkit has already updated to version 4 which is the current main branch https://github.com/etetoolkit/ete/tree/ete4. And you can easily install it with 

pip install https://github.com/etetoolkit/ete/archive/ete4.zip 

The ete3 version as I mentioned in the last email will continue serve as a branch.

It's worth to note that ete4 has changed quite a few syntax from ete3 so I recommend to have a look of our latest tutorial https://etetoolkit.github.io/ete/tutorial/tutorial_taxonomy.html

If you encounter any doubts during migrating your project using ete3 to ete4, please let me know!

Best,

Ziqi

Vishal Joshi <vjo...@ebi.ac.uk> 于2024年3月27日周三 17:42写道：

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[Marie Lefebvre]

Hi Ziqi,

I am facing the same problem. I need to use ete3 in a Galaxy pipeline but it crashes.
Are there any plans to update the installation on conda, and/or put ete4 on conda?

Best,
Marie

[Marie Lefebvre]

Hi Ziqi,
I have the same problem. I want to use ete3 in a Galaxy pipeline but it no longer works because of the download link.
Is it planned to push the change of the link on conda? Or to put ete4 on conda?

Best, 

Marie

Le mercredi 27 mars 2024 à 18:04:11 UTC+1, ziqi deng a écrit :

[dengzi...@gmail.com]

Hi! I understand! 

Let me get back to you once we updated!

Best,

Ziqi