Hi Tim!
Thank you so much for the clear explanation! 
I think I understand Hail better now.
I copy & pasted the stack trace below. Should I also put down the java stack trace?
---------------------------------------------------------------------------
Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/IPython/core/formatters.py in __call__(self, obj)
700 type_pprinters=self.type_printers,
701 deferred_pprinters=self.deferred_printers)
--> 702 printer.pretty(obj)
703 printer.flush()
704 return stream.getvalue()
/usr/local/lib/python3.6/dist-packages/IPython/lib/pretty.py in pretty(self, obj)
392 if cls is not object \
393 and callable(cls.__dict__.get('__repr__')):
--> 394 return _repr_pprint(obj, self, cycle)
395
396 return _default_pprint(obj, self, cycle)
/usr/local/lib/python3.6/dist-packages/IPython/lib/pretty.py in _repr_pprint(obj, p, cycle)
698 """A pprint that just redirects to the normal repr function."""
699 # Find newlines and replace them with p.break_()
--> 700 output = repr(obj)
701 lines = output.splitlines()
702 with p.group():
~/.local/lib/python3.6/site-packages/hail/table.py in __repr__(self)
1295
1296 def __repr__(self):
-> 1297 return self.__str__()
1298
1299 def data(self):
~/.local/lib/python3.6/site-packages/hail/table.py in __str__(self)
1292
1293 def __str__(self):
-> 1294 return self._ascii_str()
1295
1296 def __repr__(self):
~/.local/lib/python3.6/site-packages/hail/table.py in _ascii_str(self)
1318 return s
1319
-> 1320 rows, has_more, dtype = self.data()
1321 fields = list(dtype)
1322 trunc_fields = [trunc(f) for f in fields]
~/.local/lib/python3.6/site-packages/hail/table.py in data(self)
1302 row_dtype = t.row.dtype
1303 t = t.select(**{k: hl._showstr(v) for (k, v) in t.row.items()})
-> 1304 rows, has_more = t._take_n(self.n)
1305 self._data = (rows, has_more, row_dtype)
1306 return self._data
~/.local/lib/python3.6/site-packages/hail/table.py in _take_n(self, n)
1449 has_more = False
1450 else:
-> 1451 rows = self.take(n + 1)
1452 has_more = len(rows) > n
1453 rows = rows[:n]
<decorator-gen-1119> in take(self, n, _localize)
~/.local/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
612 def wrapper(__original_func, *args, **kwargs):
613 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
--> 614 return __original_func(*args_, **kwargs_)
615
616 return wrapper
~/.local/lib/python3.6/site-packages/hail/table.py in take(self, n, _localize)
2119 #"""
2120
-> 2121 return self.head(n).collect(_localize)
2122
2123 @typecheck_method(n=int)
<decorator-gen-1113> in collect(self, _localize)
~/.local/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
612 def wrapper(__original_func, *args, **kwargs):
613 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
--> 614 return __original_func(*args_, **kwargs_)
615
616 return wrapper
~/.local/lib/python3.6/site-packages/hail/table.py in collect(self, _localize)
1918 e = construct_expr(rows_ir, hl.tarray(t.row.dtype))
1919 if _localize:
-> 1920 return Env.backend().execute(e._ir)
1921 else:
1922 return e
~/.local/lib/python3.6/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed)
96 raise HailUserError(message_and_trace) from None
97
---> 98 raise e
~/.local/lib/python3.6/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed)
72 # print(self._hail_package.expr.ir.Pretty.apply(jir, True, -1))
73 try:
---> 74 result = json.loads(self._jhc.backend().executeJSON(jir))
75 value = ir.typ._from_json(result['value'])
76 timings = result['timings']
~/.local/lib/python3.6/site-packages/py4j/java_gateway.py in __call__(self, *args)
1255 answer = self.gateway_client.send_command(command)
1256 return_value = get_return_value(
-> 1257 answer, self.gateway_client, self.target_id, self.name)
1258
1259 for temp_arg in temp_args:
~/.local/lib/python3.6/site-packages/hail/backend/py4j_backend.py in deco(*args, **kwargs)
30 raise FatalError('%s\n\nJava stack trace:\n%s\n'
31 'Hail version: %s\n'
---> 32 'Error summary: %s' % (deepest, full, hail.__version__, deepest), error_id) from None
33 except pyspark.sql.utils.CapturedException as e:
34 raise FatalError('%s\n\nJava stack trace:\n%s\n'
FatalError: HailException: found allele outside of expected range [0, 2]: 3
