sokrypton / sokrypton/ColabFold
Invalid database read for database data file
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Description
Invalid database read for database data file=/home/lyy/data/db_folder/uniref30_2302_db.idx, database index=/home/lyy/data/db_folder/uniref30_2302_db.idx.index
getData: local id (4294967295) >= db size (19)
Error: Prefilter died
Traceback (most recent call last):
File "/home/lyy/data/db_folder/localcolabfold/colabfold-conda/bin/colabfold_search", line 8, in
sys.exit(main())
File "/home/lyy/data/db_folder/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 319, in main
mmseqs_search_monomer(
File "/home/lyy/data/db_folder/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 91, in mmseqs_search_monomer
run_mmseqs(mmseqs, ["search", base.joinpath("qdb"), dbbase.joinpath(uniref_db), base.joinpath("res"), base.joinpath("tmp"), "--threads", str(threads)] + search_param)
File "/home/lyy/data/db_folder/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 25, in run_mmseqs
subprocess.check_call([mmseqs] + params)
File "/home/lyy/data/db_folder/localcolabfold/colabfold-conda/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '[PosixPath('mmseqs'), 'search', PosixPath('msas/qdb'), PosixPath('/home/lyy/data/db_folder/uniref30_2302_db'), PosixPath('msas/res'), PosixPath('msas/tmp'), '--threads', '64', '--num-iterations', '3', '--db-load-mode', '0', '-a', '-e', '0.1', '--max-seqs', '10000', '--k-score', "'seq:96,prof:80'"]' returned non-zero exit status 1.
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Research direction
Start with colabfold/mmseqs/search.py and the reported mmseqs search command, then inspect how the uniref30_2302_db data and index files are selected. Reproduce the failure with the listed database paths; done means identifying the cause of the invalid database read and allowing the prefilter search to complete.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100