It worked when the flowgraph was executed by the user, maybe that satnogs user has a different approach. I had a similar error and decided to add satnogs to sudo group and ensure that it is in dialout to be able to use sdr correctly.
You are ritht @mat, waterfall.dat is saved in /tmp, which has all the editing rights. The file itself is owned by root for r/w and r for others. I changed permissions to .py files in usr/local/bin and /usr/bin and for satnogs_swig0.py. Also, dist-packages didn’t have write permission so I added it. No change in the output so far.