Docker: files missing after build - python-3.x

Question

I'm trying to build a docker container that runs a Python script. I want the code to be cloned from git when I build the image. I'm using this docker file as a base and added the following BEFORE the first line:
FROM debian:buster-slim AS intermediate
RUN apt-get update
RUN apt-get install -y git
ARG SSH_PRIVATE_KEY
RUN mkdir /root/.ssh/
RUN echo "${SSH_PRIVATE_KEY}" > /root/.ssh/id_rsa
RUN chmod 600 /root/.ssh/id_rsa
RUN touch /root/.ssh/known_hosts
RUN ssh-keyscan [git hostname] >> /root/.ssh/known_hosts
RUN git clone git#...../myApp.git
... then added the following directly after the first line:
# Copy only the repo from the intermediate image
COPY --from=intermediate /myApp /myApp
... then at the end I added this to install some dependencies:
RUN set -ex; \
apt-get update; \
apt-get install -y gcc g++ unixodbc-dev libpq-dev; \
\
pip install pyodbc; \
pip install paramiko; \
pip install psycopg2
And I changed the command to run to:
CMD ["python3 /myApp/main.py"]
If, at the end of the dockerfile before the CMD, I add the command "RUN ls -l /myApp" it lists all the files I would expect during the build. But when I use "docker run" to run the image, it gives me the following error:
docker: Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "exec: "python3 /myApp/main.py": stat python3 /myApp/main.py: no such file or directory": unknown.
My build command is:
docker build --file ./Dockerfile --tag my_app --build-arg SSH_PRIVATE_KEY="$(cat sshkey)" .
Then run with docker run my_app
There is probably some docker fundamental that I am misunderstanding, but I can't seem to figure out what it is.

Answer 1

This is hard to answer without your command line or your docker-compose.yml (if any). A recurrent mistake is to map a volume from the host into the container at a non empty location, in this case, your container files are hidden by the content of the host folder.
The last CMD should be like this:
CMD ["python3", "/myApp/main.py"]