Hi, 
I have the same problem. 

The models.py file was created by 

python manage.py inspectdb > models.py

I just copied it over into my app and modified it. My output is 

readDatabase.AuthGroupPermissions: (models.E012) 'unique_together' refers 
to the non-existent field 'group_id'.
readDatabase.AuthGroupPermissions: (models.E012) 'unique_together' refers 
to the non-existent field 'permission_id'.
readDatabase.AuthPermission: (models.E012) 'unique_together' refers to the 
non-existent field 'content_type_id'.
readDatabase.AuthUserGroups: (models.E012) 'unique_together' refers to the 
non-existent field 'group_id'.
readDatabase.AuthUserGroups: (models.E012) 'unique_together' refers to the 
non-existent field 'user_id'.
readDatabase.AuthUserUserPermissions: (models.E012) 'unique_together' 
refers to the non-existent field 'permission_id'.
readDatabase.AuthUserUserPermissions: (models.E012) 'unique_together' 
refers to the non-existent field 'user_id'.
readDatabase.Messwerte: (models.E004) 'id' can only be used as a field name 
if the field also sets 'primary_key=True'.
readDatabase.Modifikationen: (models.E004) 'id' can only be used as a field 
name if the field also sets 'primary_key=True'.
readDatabase.ProteinSequences: (models.E004) 'id' can only be used as a 
field name if the field also sets 'primary_key=True'.

The last three messages are from tables which were in the original db. All 
other messages come from tables created by django. I'm using postgresql and 
confirmed that all tables were created in my database. Below is the output 
of postgres \dt command to show all tables in the database. This happens 
when I migrate (python manage.py migrate) the changes.

 variantendatenbank=# \dt
                      Liste der Relationen
 Schema |            Name            |   Typ   |   Eigentümer    
--------+----------------------------+---------+-----------------
 public | auth_group                 | Tabelle | christoph_knapp
 public | auth_group_permissions     | Tabelle | christoph_knapp
 public | auth_permission            | Tabelle | christoph_knapp
 public | auth_user                  | Tabelle | christoph_knapp
 public | auth_user_groups           | Tabelle | christoph_knapp
 public | auth_user_user_permissions | Tabelle | christoph_knapp
 public | b_ids                      | Tabelle | christoph_knapp
 public | bedingungen                | Tabelle | christoph_knapp
 public | django_admin_log           | Tabelle | christoph_knapp
 public | django_content_type        | Tabelle | christoph_knapp
 public | django_migrations          | Tabelle | christoph_knapp
 public | django_session             | Tabelle | christoph_knapp
 public | messwerte                  | Tabelle | christoph_knapp
 public | modifikationen             | Tabelle | christoph_knapp
 public | protein_information        | Tabelle | christoph_knapp
 public | protein_sequences          | Tabelle | christoph_knapp
 public | substrate                  | Tabelle | christoph_knapp
(17 Zeilen)

If anyone could help with the errors from the django tables (maybe also 
with the problems on my tables)?

I only started yesterday to use django, so let me know if you need anything 
else.

Christoph
 
On Monday, September 14, 2015 at 7:51:58 PM UTC+2, Dmitry Homenok wrote:
>
> Hey John,
>
> Agree with James. makemigrations command doesn't create models.py file - 
> it's on your plate. But after creating models.py file and filling it with 
> your models - you have to create migration file with makemigrations command 
> and run migrate one to create all required tables, fk, etc.
>
> - Dmitry
>
> On Friday, September 11, 2015 at 10:42:03 PM UTC+3, John Emmatty wrote:
>>
>> I ran makemigrations against my legacy, MySQL database and it created 
>> models.py file for me, I copied the file to my applications package 
>> directory and ran makemigrations again after adding a table to extend the 
>> default users table. Now makemigrations is throwing following errors . I 
>> created a fresh django project which had no reference to older versions.
>>
>> SystemCheckError: System check identified some issues:
>>
>>     ERRORS:
>>     djangogettrix.AuthGroupPermissions: (models.E012) 'unique_together' 
>> refers to the non-existent field 'group_id'.
>>     djangogettrix.AuthGroupPermissions: (models.E012) 'unique_together' 
>> refers to the non-existent field 'permission_id'.
>>     djangogettrix.AuthPermission: (models.E012) 'unique_together' refers 
>> to the non-existent field 'content_type_id'.
>>     djangogettrix.AuthUserGroups: (models.E012) 'unique_together' refers 
>> to the non-existent field 'group_id'.
>>     djangogettrix.AuthUserGroups: (models.E012) 'unique_together' refers 
>> to the non-existent field 'user_id'.
>>     djangogettrix.AuthUserUserPermissions: (models.E012) 
>> 'unique_together' refers to the non-existent field 'permission_id'.
>>     djangogettrix.AuthUserUserPermissions: (models.E012) 
>> 'unique_together' refers to the non-existent field 'user_id'.
>>     djangogettrix.RolesUsers: (models.E012) 'unique_together' refers to 
>> the non-existent field 'role_id'.
>>     djangogettrix.RolesUsers: (models.E012) 'unique_together' refers to 
>> the non-existent field 'user_id'.
>>
>> Kindly help me by throwing some light on this.
>>
>

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