Error of "sqlite3.OperationalError: database is locked"

[Cheng Fang]

Hi all,

I was trying to use the mmpdb version 3 for the fragmentation. However, I came across an error when implementing it on Linux:

The code I ran is mmpdb fragment test_data.smi -o test_data.fragdb

The error is:
`Failed to execute the following SQL:
-- Version 3.0 switched to a SQLite database to store the fragments.
-- Earlier versions used JSON-Lines.
-- The SQLite database improves I/O time, reduces memory use, and
-- simplifies the development of fragment analysis tools.

-- NOTE: There is configuration information in three files!
-- 1) fragment_types.py -- the data types
-- 2) fragment_schema.sql -- (this file) defines the SQL schema
-- 3) fragment_db.py -- defines the mapping from SQL to the data types

CREATE TABLE options (
id INTEGER NOT NULL,
version INTEGER,
cut_smarts VARCHAR(1000),
max_heavies INTEGER,
max_rotatable_bonds INTEGER,
method VARCHAR(20),
num_cuts INTEGER,
rotatable_smarts VARCHAR(1000),
salt_remover VARCHAR(200),
min_heavies_per_const_frag INTEGER,
min_heavies_total_const_frag INTEGER,
max_up_enumerations INTEGER,
PRIMARY KEY (id)
);
Traceback (most recent call last):
File "/miniconda3/envs/mmpdb31/bin/mmpdb", line 8, in
sys.exit(main())
File "/.local/lib/python3.9/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/.local/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/.local/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/.local/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/.local/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/miniconda3/envs/mmpdb31/lib/python3.9/site-packages/mmpdblib/cli/fragment_click.py", line 215, in make_fragment_options_wrapper
return command(**kwargs)
File "/miniconda3/envs/mmpdb31/lib/python3.9/site-packages/mmpdblib/cli/smi_utils.py", line 98, in make_input_options_wrapper
return command(**kwargs)
File "/.local/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/miniconda3/envs/mmpdb31/lib/python3.9/site-packages/mmpdblib/cli/fragment.py", line 256, in fragment
with fragment_db.open_fragment_writer(
File "/miniconda3/envs/mmpdb31/lib/python3.9/site-packages/mmpdblib/fragment_db.py", line 372, in open_fragment_writer
init_fragdb(c, options)
File "/miniconda3/envs/mmpdb31/lib/python3.9/site-packages/mmpdblib/fragment_db.py", line 92, in init_fragdb
schema._execute_sql(c, get_schema_template())
File "/miniconda3/envs/mmpdb31/lib/python3.9/site-packages/mmpdblib/schema.py", line 129, in _execute_sql
c.execute(statement)
sqlite3.OperationalError: database is locked`

It probably has nothing to do with the MMPDB-v3 program since it is running fine on my Mac. If anyone has some advice/suggestions on how to solve it, it would be highly appreciated.

Thanks,
Cheng

[Cheng Fang]

I figured out it was my Linux system error. It works when I changed the file location. Let me close the ticket