Open BinhongLiu opened 1 year ago
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.
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?
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.
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?
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
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.
@pengtb, can you confirm that the second link DOES NOT work for you?
@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.
So the second link works sometimes and the first link works always?
@pengtb any update on this?
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