SQLite issue when running through snakemake

[domenico-simone]

• mtoolnote version: 0.2.0
• Python version: 3.6.7
• Operating System: CentOS Linux release 7.8.2003 (Core)

Description

Running mtoolnote calling the function is ok. Run it through snakemake, succeeds but return this warning:

Exception during reset or similar
Traceback (most recent call last):
  File "/crex/proj/uppstore2018116/domenico/conda_envs/mtoolbox/lib/python3.6/site-packages/sqlalchemy/pool.py", line 731, in _finalize_fairy
    fairy._reset(pool)
  File "/crex/proj/uppstore2018116/domenico/conda_envs/mtoolbox/lib/python3.6/site-packages/sqlalchemy/pool.py", line 918, in _reset
    pool._dialect.do_rollback(self)
  File "/crex/proj/uppstore2018116/domenico/conda_envs/mtoolbox/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 486, in do_rollback
    dbapi_connection.rollback()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 47413066213120 and this is thread id 47411398409856.
Exception closing connection <sqlite3.Connection object at 0x2b1f36fc8730>
Traceback (most recent call last):
  File "/crex/proj/uppstore2018116/domenico/conda_envs/mtoolbox/lib/python3.6/site-packages/sqlalchemy/pool.py", line 731, in _finalize_fairy
    fairy._reset(pool)
  File "/crex/proj/uppstore2018116/domenico/conda_envs/mtoolbox/lib/python3.6/site-packages/sqlalchemy/pool.py", line 918, in _reset
    pool._dialect.do_rollback(self)
  File "/crex/proj/uppstore2018116/domenico/conda_envs/mtoolbox/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 486, in do_rollback
    dbapi_connection.rollback()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 47413066213120 and this is thread id 47411398409856.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/crex/proj/uppstore2018116/domenico/conda_envs/mtoolbox/lib/python3.6/site-packages/sqlalchemy/pool.py", line 326, in _close_connection
    self._dialect.do_close(connection)
  File "/crex/proj/uppstore2018116/domenico/conda_envs/mtoolbox/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 492, in do_close
    dbapi_connection.close()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 47413066213120 and this is thread id 47411398409856.