sokrypton / sokrypton/ColabFold
Running setup_databases.sh with error
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Description
Expected Behavior
Expected to run the setup_databases.sh script without errors.
Current Behavior
When running line 78: rsync -rlpt -v -z --delete --port=33444 rsync.wwpdb.org::ftp/data/structures/divided/mmCIF/ pdb/divided I get the following error:
rsync: safe_read failed to read 1 bytes [Receiver]: Connection timed out (110)
rsync error: error in rsync protocol data stream (code 12) at io.c(276) [Receiver=3.1.3]
Not sure what the problem is as the error is pretty non-descriptive. Is this a known problem/bug? I have tried multiple times so I don't think the problem is connectivity but I am not completely sure.
Your Environment
Trying to run ColabFold Search using the guide (https://colabfold.mmseqs.com) using a freshly installed conda environment with MMSeqs2 installed on a remote server.
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 setup_databases.sh, especially line 78 and its rsync command, then reproduce the timeout described in the issue. Check whether the script can complete the database download; done means the command runs without the reported rsync protocol error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100