sokrypton / sokrypton/ColabFold
Error extracting the uniref30
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
Hi,
I am trying to follow the steps to download the db to run the MSA locally. I have used the download script to get uniref30. The download seems to have been completed successfully, but the extraction of the .tar fails. Any suggestions on how to address this?
Thanks
uniref30_2302.tar.gz 100%[==================================>] 95.85G 4.12MB/s in 6h 20m
2024-05-01 23:17:52 (4.29 MB/s) - ‘uniref30_2302.tar.gz’ saved [102918187842/102918187842]
+ set -e
+ return 0
+ tar xzvf uniref30_2302.tar.gz
uniref30_2302.md5sum
tar: uniref30_2302.md5sum: Cannot change ownership to uid 528745, gid 9100: Invalid argument
uniref30_2302.tsv
tar: uniref30_2302.tsv: Cannot change ownership to uid 528745, gid 9100: Invalid argument
uniref30_2302_h.tsv
tar: uniref30_2302_h.tsv: Cannot change ownership to uid 528745, gid 9100: Invalid argument
uniref30_2302_aln.tsv
tar: uniref30_2302_aln.tsv: Cannot change ownership to uid 528745, gid 9100: Invalid argument
uniref30_2302_seq.tsv
tar: uniref30_2302_seq.tsv: Cannot change ownership to uid 528745, gid 9100: Invalid argument
uniref30_2302_db_mapping
tar: uniref30_2302_db_mapping: Cannot change ownership to uid 528745, gid 9100: Invalid argument
uniref30_2302_db_taxonomy
tar: uniref30_2302_db_taxonomy: Cannot change ownership to uid 528745, gid 9100: Invalid argument
tar: Exiting with failure status due to previous errors
This is the list of files downloaded
ls -l /root/colabfold_db
.rw------- 337 root 22 May 2023 uniref30_2302.md5sum
.rw-rw-r-- 103G root 22 May 2023 uniref30_2302.tar.gz
.rw------- 9.1G root 16 May 2023 uniref30_2302.tsv
.rw------- 31G root 16 May 2023 uniref30_2302_aln.tsv
.rw------- 5.8G root 22 May 2023 uniref30_2302_db_mapping
.rw------- 668M root 22 May 2023 uniref30_2302_db_taxonomy
.rw------- 46G root 16 May 2023 uniref30_2302_h.tsv
.rw------- 137G root 16 May 2023 uniref30_2302_seq.tsv
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
Reproduce the download and extraction commands shown in the issue, then inspect the database download script around its tar invocation. Confirm how the uniref30 archive behaves in the target environment and whether the project documents this ownership error; done means establishing and recording a reproducible resolution for extraction.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell
- Domain
- bioinformatics, databases
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100