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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  3. Fork the repository and make your change on a branch.
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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

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