sokrypton / sokrypton/ColabFold

Database . does not exist

Open
#748 7 comments 0 reactions 0 assignees View on GitHub

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'm encountering an issue while trying to run colabfold_search.
I would appreciate any suggestions you might have for resolving it. Thank you in advance!

“colabfold_search test.fasta ./colabfold_db/ test --af3-json --use-templates 1
INFO:colabfold.mmseqs.search:Running mmseqs createdb test/query.fas test/qdb --shuffle 0
createdb test/query.fas test/qdb --shuffle 0

Converting sequences

Time for merging to qdb_h: 0h 0m 0s 1ms
Time for merging to qdb: 0h 0m 0s 0ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 6ms
Traceback (most recent call last):
File "/data/igem/dxxu/ColabFold_MMseqsGPU/localcolabfold/colabfold-conda/bin/colabfold_search", line 8, in
sys.exit(main())
File "/data/igem/dxxu/ColabFold_MMseqsGPU/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 461, in main
mmseqs_search_monomer(
File "/data/igem/dxxu/ColabFold_MMseqsGPU/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 93, in mmseqs_search_monomer
raise FileNotFoundError(f"Database {db} does not exist")
FileNotFoundError: Database . does not exist“

Contributor guide

Open the contributing guide

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 the shown colabfold_search command and the traceback location in colabfold/mmseqs/search.py at line 93. Trace how the command arguments produce the database value '.', then reproduce the search and verify that the database path is resolved correctly and the command completes.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.