sokrypton / sokrypton/ColabFold
Database . does not exist
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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
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 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