You are trying to debug a Python program that uses shell (or Bash) commands. The shell or Bash commands work when they are called with Python's subprocess.check_output. They do not work when called directly from the Linux command prompt. What is wrong?
Normally I.T. professionals can get the Linux (Bash or shell) commands to work without as many moving parts. In some instances the Python script that executes the Bash commands seem to help the reliability of the commands. Sometimes you inherit code that you must maintain. In these instances you need to reverse engineer the code. These solutions below were made for the scenario where the Python program works, but when the individual Linux command is run separately without Python, the Linux command fails by itself.
1. Does the Python code have backslashes "\"? These are used as "escape" characters so the parsing of the Bash commands will be done properly. Some quotation marks are needed in Bash commands. The Python interpreter may not know if it should parse the punctuation itself or save it for the Bash command. It may be necessary to have these escape characters in the Python program. However these may cause the Bash commands to fail when run outside the context of a Python program (e.g., if they are lifted verbatim and run interactively for testing purposes).
2. Are there environment variables that are involved? It could be that manually running the Bash commands reveals that your user context is different from the Python invocation of such commands. As a debugging tool, compare the output of "env" run interactively to that run in the Python program. Some utilities in Linux may need their full subdirectory path to be called to work via Python subprocess.check_output invocations.
3. Does the Python code do some sort of authentication process? When trying to manually troubleshoot Linux commands used in a Python program, see if there are previous lines of code in the Python program that log into a system. Do not get ahead of yourself or make assumptions. Some Linux commands may only work if the sequence is exact.