Issues with sqlite3 and initiating cblaster

[pksun1]

Hi,

I'm not very good with python, but I most definitely would like to use cblaster! However, I've run into an issue where I can't seem to initiate the program. Please see below the traceback logs

(myenv) C:\Users\Phillip\env\myenv\Scripts>cblaster
Traceback (most recent call last):
File "c:\users\phillip\appdata\local\programs\python\python38\lib\runpy.py", line 194, in _run_module_as_main
return run_code(code, main_globals, None,
File "c:\users\phillip\appdata\local\programs\python\python38\lib\runpy.py", line 87, in run_code
exec(code, run_globals)
File "C:\Users\Phillip\AppData\Local\Programs\Python\Python38\Scripts\cblaster.exe_main.py", line 4, in
File "c:\users\phillip\appdata\local\programs\python\python38\lib\site-packages\cblaster\main.py", line 11, in
from cblaster import (
File "c:\users\phillip\appdata\local\programs\python\python38\lib\site-packages\cblaster\context.py", line 44, in
from cblaster import database
File "c:\users\phillip\appdata\local\programs\python\python38\lib\site-packages\cblaster\database.py", line 9, in
import genomicsqlite
File "c:\users\phillip\appdata\local\programs\python\python38\lib\site-packages\genomicsqlite_init.py", line 30, in
_MEMCONN.load_extension(_DLL)
sqlite3.OperationalError: The specified module could not be found.

Is this something off with cblaster? or is it an error on a dependency, or another program that cblaster relies on?

I've updated sqlite3 to it's most current version as well, which would be:

sqlite3.sqlite_version
'3.38.5'

Please let me know how might I address this. I'm currently using Windows 11, 64bit.

[gamcil]

Hi @pksun1, I think the issue is an SQL related library added with the latest release (genomicsqlite). For now you could revert to an older version which should work:

pip install --upgrade cblaster==1.3.12

I also run into the same issue on OSX 12.4, M1 chip, using within a Conda environment. Not sure if it has something to do with Python sqlite not allowing loadable extensions, or genomicsqlite itself.. @brymerr921 Any ideas? I guess an easy quick fix is just to add a fallback to the regular sqlite3 built in library if importing genomicsqlite fails.

[pksun1]

Thank you so much!!! I've been trying to work with alternative programs but I had really wanted to utilize cblaster, now I have it running my first search! You totally salvaged my weekend! Thanks!