sokrypton / sokrypton/ColabFold

Downloading colabfold Database issues

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Description

I have been trying to download the colabfold databases (colabfold.mmseqs.com) to run setup_databases.sh for a couple of weeks now without success. Aria2c used through setup script or by command line gives "errorCode=8 Invalid range header.

Download by wget is pretty slow (~100 KB/s), has to be restarted several times and resulting file errors on decompression. Anyone else having this problem?

Expected Behavior

running setup_databases.sh downloads and installs colabfold database from colabfold.mmseqs.com

Current Behavior

not able to download larger databases uniref30_2202.tar.gz or colabfold_envdb_202108.tar.gz with script or with aria2c, wget download wrong md5checksum and fails on decompression

Steps to Reproduce (for bugs)

./setup_databases.sh
aria2c -c -x 8 https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2202.tar.gz

ColabFold Output (for bugs)

errorCode=8 Invalid range header

Your Environment

CentOS7

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with setup_databases.sh and reproduce the aria2c command against the two named database URLs on CentOS 7. Check the download behavior, resulting MD5 checksums, and decompression failures reported in the issue. Done means the script can reliably download and install uniref30_2202.tar.gz and colabfold_envdb_202108.tar.gz without invalid range errors or corrupted files.

Written by the indexing model from the issue text.

Assessment

Tech stack
shell
Domain
bioinformatics, devops
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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