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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
The text was updated successfully, but these errors were encountered:
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)?
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
The text was updated successfully, but these errors were encountered: