makedb always results in 'sqlite3.OperationalError: database is locked'

[jjsanchezgil]

Hi,

I have been trying to create a local database but sqlite3 keeps showing this error.

$ cblaster makedb -n test genomic.gff

Importing genomicsqlite failed, falling back to SQLite3
[12:06:13] INFO - Starting makedb module
[12:06:13] INFO - Initialising cblaster SQLite3 database to test.sqlite3
Traceback (most recent call last):
File "/opt/conda/anaconda3/envs/cblaster-env/bin/cblaster", line 10, in
sys.exit(main())
File "/opt/conda/anaconda3/envs/cblaster-env/lib/python3.8/site-packages/cblaster/main.py", line 422, in main
database.makedb(
File "/opt/conda/anaconda3/envs/cblaster-env/lib/python3.8/site-packages/cblaster/database.py", line 180, in makedb
init_sqlite_db(sqlite_path, force=force)
File "/opt/conda/anaconda3/envs/cblaster-env/lib/python3.8/site-packages/cblaster/database.py", line 39, in init_sqlite_db
con.executescript(sql.SCHEMA)
sqlite3.OperationalError: database is locked

When I install genomicsqlite, there is still a different error (probably with the same origin)

$ cblaster makedb -f -n test genomic.gff

[12:22:06] INFO - Starting makedb module
[12:22:06] INFO - Pre-existing files found, overwriting
[12:22:06] INFO - Overwriting pre-existing file at test.sqlite3
Traceback (most recent call last):
File "/opt/conda/anaconda3/envs/cblaster-env/bin/cblaster", line 10, in
sys.exit(main())
^^^^^^
File "/opt/conda/anaconda3/envs/cblaster-env/lib/python3.11/site-packages/cblaster/main.py", line 423, in main
database.makedb(
File "/opt/conda/anaconda3/envs/cblaster-env/lib/python3.11/site-packages/cblaster/database.py", line 185, in makedb
init_sqlite_db(sqlite_path, force=force)
File "/opt/conda/anaconda3/envs/cblaster-env/lib/python3.11/site-packages/cblaster/database.py", line 43, in init_sqlite_db
with SQLITE.connect(str(path)) as con:
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/juanjo/.local/lib/python3.11/site-packages/genomicsqlite/init.py", line 73, in connect
conn = sqlite3.connect(uri, uri=True, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
sqlite3.OperationalError: unable to open database file

In my folder I have 3 files: genomic.fasta, genomic.gff, and genomic.gbff, but it doesn't matter if you try to build a database with only one file, like in this case, or with thousands, and either from gff or gbff. I tried installing cblaster from conda and with pip, but still the same error. What could be the source of the problem? Thanks

[gamcil]

Not sure what is happening unfortunately, I haven't run into this and can't reproduce it. Usually this error would come from something also interacting with the SQLite database file at the same time (e.g. via a DB browser/through the terminal). Maybe you have some rogue process in the background causing it to lock (https://stackoverflow.com/a/3481134)?

[mcn3159]

Hi, any chance someone solved this issue? I'm getting the same error regarding sqlite being unable to open database file.