A shorter reproducer;

>>> import sys
>>> sys.modules.clear()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
RuntimeError: lost builtins module
>>> import _ast
>>> import gc
>>> gc.collect()
Modules/gcmodule.c:114: gc_decref: Assertion "gc_get_refs(g) > 0" failed: refcount is too small
Enable tracemalloc to get the memory block allocation traceback

object address  : 0x7f4c22f843b0
object refcount : 2
object type     : 0x5605f3385660
object type name: module
object repr     : <module '_ast' (built-in)>

Fatal Python error: _PyObject_AssertFailed: _PyObject_AssertFailed
Python runtime state: initialized

Current thread 0x00007f4c23a5d280 (most recent call first):
  File "<stdin>", line 1 in <module>
[1]    21945 abort (core dumped)  ./python