database download manually

[BinhongLiu]

Expected Behavior

Could the pre-processed PDB and Alphafold/Swiss-Prot database be downloaded manually?

Current Behavior

Could not download the database with script foldseek databases PDB pdb tmp. And the link https://foldseek.steineggerlab.workers.dev/pdb100.tar.gz could not be opened, either.

Steps to Reproduce (for bugs)

foldseek databases PDB pdb tmp

Foldssek Output (for bugs)

Create directory tmp databases PDB pdb tmp

MMseqs Version: 5.53465f0 Tsv false Force restart with latest tmp false Remove temporary files false Compressed 0 Threads 8 Verbosity 3

04/15 18:24:45 [NOTICE] Downloading 1 item(s) Download Progress Summary as of Sat Apr 15 18:25:46 2023

[#f34170 0B/0B CN:1 DL:0B] FILE: tmp/5535929346258916704/pdb.tar.gz

Download Progress Summary as of Sat Apr 15 18:26:46 2023

[#f34170 0B/0B CN:1 DL:0B] FILE: tmp/5535929346258916704/pdb.tar.gz

Download Progress Summary as of Sat Apr 15 18:27:46 2023

[#f34170 0B/0B CN:1 DL:0B] FILE: tmp/5535929346258916704/pdb.tar.gz

Download Progress Summary as of Sat Apr 15 18:28:46 2023

[#f34170 0B/0B CN:1 DL:0B] FILE: tmp/5535929346258916704/pdb.tar.gz

Download Progress Summary as of Sat Apr 15 18:29:46 2023

[#f34170 0B/0B CN:1 DL:0B] FILE: tmp/5535929346258916704/pdb.tar.gz

[#f34170 0B/0B CN:1 DL:0B]
04/15 18:29:51 [ERROR] CUID#7 - Download aborted. URI=https://foldseek.steineggerlab.workers.dev/pdb100.tar.gz Exception: [AbstractCommand.cc:340] errorCode=2 Timeout.

04/15 18:29:51 [NOTICE] Download GID#f34170de50d28f9a not complete: tmp/5535929346258916704/pdb.tar.gz

Download Results: gid |stat|avg speed |path/URI ======+====+===========+======================================================= f34170|ERR | 0B/s|tmp/5535929346258916704/pdb.tar.gz

Status Legend: (ERR):error occurred.

aria2 will resume download if the transfer is restarted. If there are any errors, then see the log file. See '-l' option in help/man page for details. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:02:08 --:--:-- 0curl: (7) Failed to connect to foldseek.steineggerlab.workers.dev port 443: Connection timed out --2023-04-15 18:32:00-- https://foldseek.steineggerlab.workers.dev/pdb100.tar.gz Resolving foldseek.steineggerlab.workers.dev (foldseek.steineggerlab.workers.dev)... 31.13.91.6, 2a03:2880:f10d:83:face:b00c:0:25de Connecting to foldseek.steineggerlab.workers.dev (foldseek.steineggerlab.workers.dev)|31.13.91.6|:443... failed: Connection timed out. Connecting to foldseek.steineggerlab.workers.dev (foldseek.steineggerlab.workers.dev)|2a03:2880:f10d:83:face:b00c:0:25de|:443... failed: Network is unreachable. Error: Could not download https://foldseek.steineggerlab.workers.dev/pdb100.tar.gz to tmp/5535929346258916704/pdb.tar.gz

Context

A virtual environment was created and the foldseek was installed with conda conda install -c conda-forge -c bioconda foldseek.

Your Environment

Linux

[milot-mirdita]

It seems to work correctly for me. Could you provide any details about your network connection? Do you have an alternative internet connection or VPN to try to download? I don't see a reason why the download should not work.

[BinhongLiu]

Thanks for your reply and kind help! I also could not open the https://foldseek.steineggerlab.workers.dev/pdb100.tar.gz with the edge browser. I think it might because of the network barrier in my country. Do you have any alternate website to download the database, like ftp, cloud drive, or something other?

[milot-mirdita]

This seems to be a known issue, that I was not aware: https://community.cloudflare.com/t/worker-is-not-available-in-china/497419 https://community.cloudflare.com/t/cloudflare-workers-suspected-of-being-blocked-in-china/382155

I guess we could try to set up a custom domain name. I can see how difficult that is maybe next week. Until then I don't really have a good solution for you.

[jiaweiguan]

This seems to be a known issue, that I was not aware: https://community.cloudflare.com/t/worker-is-not-available-in-china/497419 https://community.cloudflare.com/t/cloudflare-workers-suspected-of-being-blocked-in-china/382155

I guess we could try to set up a custom domain name. I can see how difficult that is maybe next week. Until then I don't really have a good solution for you.

Hi, @milot-mirdita , I also encountered the same problem. Is there a new download address available now?

[milot-mirdita]

Could either of you @jiaweiguan or @BinhongLiu please try if the following URL works: https://foldseek-cdn.mmseqs.org/pdb100.tar.gz

Please also check that the original URL DOES NOT work: https://foldseek.steineggerlab.workers.dev/pdb100.tar.gz

[pengtb]

Could either of you @jiaweiguan or @BinhongLiu please try if the following URL works: https://foldseek-cdn.mmseqs.org/pdb100.tar.gz

Please also check that the original URL DOES NOT work: https://foldseek.steineggerlab.workers.dev/pdb100.tar.gz

Thanks. It works.

[milot-mirdita]

@pengtb, can you confirm that the second link DOES NOT work for you?

[pengtb]

@pengtb, can you confirm that the second link DOES NOT work for you?

not really. it works just now. it seems that the original one is just unstable in CN somehow.

[milot-mirdita]

So the second link works sometimes and the first link works always?

[martin-steinegger]

@pengtb any update on this?