[BUG] Error on "ov run exampleinput -a clinvar -t vcf"

[lopatich]

2022/11/27 23:59:37 oakvar.mapper input file: /home/pavlov_stud/second/project/exampleinput.crv
Exception in thread Thread-3:
Traceback (most recent call last):
File "/usr/lib/python3.8/threading.py", line 932, in _bootstrap_inner
self.run()
File "/usr/lib/python3.8/threading.py", line 870, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/python3.8/multiprocessing/pool.py", line 576, in _handle_results
task = get()
File "/usr/lib/python3.8/multiprocessing/connection.py", line 251, in recv
return _ForkingPickler.loads(buf.getbuffer())
ModuleNotFoundError: No module named 'pysqlite2'

• OS: Ubuntu
• OakVar Version v2.6.3

[rkimoakbioinformatics]

Hi @lopatich , sorry for this late reply. I was busy with the new release (v2.7). The error seems to be related to your system environment, since OakVar does not use pysqlite2. Did you install OakVar with pip install oakvar? It should use sqlite3 module already included in Python 3. Some suggestions are:

• Try installing some libraries as recommended is ImportError: No module named 'pysqlite2' jupyterhub/jupyterhub#464 and https://stackoverflow.com/questions/45565290/jupyter-missing-sqlite3-and-pysqlite2.
• Try a clean Python 3 environment with conda or virtualenv (Python 3.8 or higher).

Let me know if the above did not work.

[rkimoakbioinformatics]

@lopatich Hi, do you still experience the issue?