sokrypton / sokrypton/ColabFold
Alternative database download location?
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Description
Are the databases on https://colabfold.mmseqs.com/ available anywhere else, like AWS? Download speeds are very slow and seem to be limited by at the mmseqs.com end.
Expected Behavior
Download UniRef30 database in about an hour if D/L speed was 150Mbps.
Current Behavior
~ 40 hours estimated to download UniRef30 from various institutions, all with 10Gbps internet connections.
Steps to Reproduce (for bugs)
Download: http://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2103.tar.gz
ColabFold Output (for bugs)
Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.
Context
Download of databases listed on https://colabfold.mmseqs.com/ is extremely slow. Attempted from multiple locations, different days, all with same result.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the database links on colabfold.mmseqs.com and the UniRef30 URL in the report; compare their availability and download performance from a suitable mirror. Done means identifying an accessible alternate location or documenting that none is available, with a reproducible download target and speed.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, databases
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100