[Python] Using subprocess.call() within Pycharm Python virtualenv -- how to deactivate venv...

I am using Pycharm for Python development. Code is running in Pycharm venv from where I want to call a bash script which activates and deactivates conda environments (this one: https://github.com/lykaust15/DeepSimulator).

So I need to deactivate the Pycharm venv when calling the script via subprocess.call(), as far as I understand. Otherwise I get errors. How do I do this?

My call is:

result = subprocess.call([deppsim_path, "-i", fasta, "-c", "4",
"-C", "1", "-n", "100",
"-H", os.path.dirname(deppsim_path),
"-o", tmp_path], shell=False)


EDIT:

Some of the errors:

/home/user/path/bin/venv/bin/python /home/user/path/bin/sim_seq.py
Pre-process input genome...
/home/user/path/bin/DeepSimulator/deep_simulator.sh: Zeile 207: deactivate: Datei oder Verzeichnis nicht gefunden
Pre-process input genome done!
Executing the preprocessing step...
Traceback (most recent call last):
File "/home/user/path/bin/DeepSimulator/util/genome_sampling.py", line 5, in <module>
import scipy.stats as st
ImportError: No module named scipy.stats

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