The tables are not in an explicitly named schema. By default, it uses the 
schema of the user logged in. Looking at the debug output on the console, I 
can see that it uses the correct schema i.e. SYSTEM.

I set the logging to debug and went through the whole process. I'll attach 
the entire output. I'm using flask-migrate, which just puts a nice wrapper 
around alembic for flask development purposes. So the 'migrate' command is 
a proxy an alias for autogenerate. 'upgrade' and 'downgrade' are the same. 
So please see the output attached. Thank you.

Nana

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(sqliteenv)Nanas-MacBook-Pro:data_upload_sqlite okyere$ python manage.py db init
  Creating directory /Users/okyere/Repos/data_upload_sqlite/migrations ... done
  Creating directory /Users/okyere/Repos/data_upload_sqlite/migrations/versions 
... done
  Generating /Users/okyere/Repos/data_upload_sqlite/migrations/alembic.ini ... 
done
  Generating /Users/okyere/Repos/data_upload_sqlite/migrations/env.py ... done
  Generating /Users/okyere/Repos/data_upload_sqlite/migrations/README ... done
  Generating /Users/okyere/Repos/data_upload_sqlite/migrations/script.py.mako 
... done
  Please edit configuration/connection/logging settings in 
'/Users/okyere/Repos/data_upload_sqlite/migrations/alembic.ini' before 
proceeding.
(sqliteenv)Nanas-MacBook-Pro:data_upload_sqlite okyere$ python manage.py db 
migrate
INFO  [sqlalchemy.engine.base.Engine] SELECT USER FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
DEBUG [sqlalchemy.engine.base.Engine] Col ('USER',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('SYSTEM',)
INFO  [sqlalchemy.engine.base.Engine] SELECT CAST('test plain returns' AS 
VARCHAR(60 CHAR)) AS anon_1 FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] SELECT CAST('test unicode returns' AS 
NVARCHAR2(60)) AS anon_1 FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [alembic.runtime.migration] Context impl OracleImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
INFO  [sqlalchemy.engine.base.Engine] SELECT table_name FROM all_tables WHERE 
table_name = :name AND owner = :schema_name
INFO  [sqlalchemy.engine.base.Engine] {'schema_name': 'SYSTEM', 'name': 
'ALEMBIC_VERSION'}
DEBUG [sqlalchemy.engine.base.Engine] Col ('TABLE_NAME',)
INFO  [sqlalchemy.engine.base.Engine] SELECT table_name FROM all_tables WHERE 
table_name = :name AND owner = :schema_name
INFO  [sqlalchemy.engine.base.Engine] {'schema_name': 'SYSTEM', 'name': 
'ALEMBIC_VERSION'}
DEBUG [sqlalchemy.engine.base.Engine] Col ('TABLE_NAME',)
INFO  [sqlalchemy.engine.base.Engine] 
CREATE TABLE alembic_version (
        version_num VARCHAR2(32 CHAR) NOT NULL
)


INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] COMMIT
INFO  [sqlalchemy.engine.base.Engine] SELECT table_name FROM all_tables WHERE 
nvl(tablespace_name, 'no tablespace') NOT IN ('SYSTEM', 'SYSAUX') AND OWNER = 
:owner AND IOT_NAME IS NULL AND DURATION IS NULL
INFO  [sqlalchemy.engine.base.Engine] {'owner': 'SYSTEM'}
DEBUG [sqlalchemy.engine.base.Engine] Col ('TABLE_NAME',)
INFO  [alembic.autogenerate.compare] Detected added table 'dut_departments'
INFO  [alembic.autogenerate.compare] Detected added table 'dut_field_types'
INFO  [alembic.autogenerate.compare] Detected added table 'dut_uploadslog'
INFO  [alembic.autogenerate.compare] Detected added table 'dut_tables_info'
INFO  [alembic.autogenerate.compare] Detected added table 'dut_fields'
  Generating 
/Users/okyere/Repos/data_upload_sqlite/migrations/versions/34dacf7310ff_.py ... 
done
(sqliteenv)Nanas-MacBook-Pro:data_upload_sqlite okyere$ python manage.py db 
upgrade
INFO  [sqlalchemy.engine.base.Engine] SELECT USER FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
DEBUG [sqlalchemy.engine.base.Engine] Col ('USER',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('SYSTEM',)
INFO  [sqlalchemy.engine.base.Engine] SELECT CAST('test plain returns' AS 
VARCHAR(60 CHAR)) AS anon_1 FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] SELECT CAST('test unicode returns' AS 
NVARCHAR2(60)) AS anon_1 FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [alembic.runtime.migration] Context impl OracleImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
INFO  [sqlalchemy.engine.base.Engine] SELECT table_name FROM all_tables WHERE 
table_name = :name AND owner = :schema_name
INFO  [sqlalchemy.engine.base.Engine] {'schema_name': 'SYSTEM', 'name': 
'ALEMBIC_VERSION'}
DEBUG [sqlalchemy.engine.base.Engine] Col ('TABLE_NAME',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('ALEMBIC_VERSION',)
INFO  [sqlalchemy.engine.base.Engine] SELECT alembic_version.version_num 
FROM alembic_version
INFO  [sqlalchemy.engine.base.Engine] {}
DEBUG [sqlalchemy.engine.base.Engine] Col ('VERSION_NUM',)
INFO  [sqlalchemy.engine.base.Engine] SELECT table_name FROM all_tables WHERE 
table_name = :name AND owner = :schema_name
INFO  [sqlalchemy.engine.base.Engine] {'schema_name': 'SYSTEM', 'name': 
'ALEMBIC_VERSION'}
DEBUG [sqlalchemy.engine.base.Engine] Col ('TABLE_NAME',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('ALEMBIC_VERSION',)
INFO  [alembic.runtime.migration] Running upgrade  -> 34dacf7310ff, empty 
message
INFO  [sqlalchemy.engine.base.Engine] 
CREATE TABLE dut_departments (
        id INTEGER NOT NULL, 
        name VARCHAR2(120 CHAR) NOT NULL, 
        PRIMARY KEY (id), 
        UNIQUE (name)
)


INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] COMMIT
INFO  [sqlalchemy.engine.base.Engine] 
CREATE TABLE dut_field_types (
        id INTEGER NOT NULL, 
        name VARCHAR2(120 CHAR) NOT NULL, 
        python_type VARCHAR2(120 CHAR), 
        python_import VARCHAR2(120 CHAR), 
        PRIMARY KEY (id), 
        UNIQUE (name)
)


INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] COMMIT
INFO  [sqlalchemy.engine.base.Engine] 
CREATE TABLE dut_uploadslog (
        id INTEGER NOT NULL, 
        user_name VARCHAR2(120 CHAR) NOT NULL, 
        user_cwsid VARCHAR2(120 CHAR) NOT NULL, 
        last_name VARCHAR2(120 CHAR), 
        file_name VARCHAR2(120 CHAR) NOT NULL, 
        destination_table VARCHAR2(120 CHAR) NOT NULL, 
        timestamp TIMESTAMP NOT NULL, 
        PRIMARY KEY (id)
)


INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] COMMIT
INFO  [sqlalchemy.engine.base.Engine] 
CREATE TABLE dut_tables_info (
        id INTEGER NOT NULL, 
        descriptive_name VARCHAR2(120 CHAR) NOT NULL, 
        table_name VARCHAR2(30 CHAR) NOT NULL, 
        department_id INTEGER, 
        PRIMARY KEY (id), 
        FOREIGN KEY(department_id) REFERENCES dut_departments (id), 
        UNIQUE (descriptive_name), 
        UNIQUE (table_name)
)


INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] COMMIT
INFO  [sqlalchemy.engine.base.Engine] 
CREATE TABLE dut_fields (
        id INTEGER NOT NULL, 
        name VARCHAR2(120 CHAR) NOT NULL, 
        fieldtype_id INTEGER, 
        tableinfo_id INTEGER, 
        PRIMARY KEY (id), 
        FOREIGN KEY(fieldtype_id) REFERENCES dut_field_types (id), 
        FOREIGN KEY(tableinfo_id) REFERENCES dut_tables_info (id)
)


INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] COMMIT
INFO  [sqlalchemy.engine.base.Engine] INSERT INTO alembic_version (version_num) 
VALUES ('34dacf7310ff')
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] COMMIT
(sqliteenv)Nanas-MacBook-Pro:data_upload_sqlite okyere$ ### About to do another 
autogenerate since I deleted a column in one of the models
(sqliteenv)Nanas-MacBook-Pro:data_upload_sqlite okyere$ python manage.py db 
migrate
INFO  [sqlalchemy.engine.base.Engine] SELECT USER FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
DEBUG [sqlalchemy.engine.base.Engine] Col ('USER',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('SYSTEM',)
INFO  [sqlalchemy.engine.base.Engine] SELECT CAST('test plain returns' AS 
VARCHAR(60 CHAR)) AS anon_1 FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] SELECT CAST('test unicode returns' AS 
NVARCHAR2(60)) AS anon_1 FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [alembic.runtime.migration] Context impl OracleImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
INFO  [sqlalchemy.engine.base.Engine] SELECT table_name FROM all_tables WHERE 
table_name = :name AND owner = :schema_name
INFO  [sqlalchemy.engine.base.Engine] {'name': 'ALEMBIC_VERSION', 
'schema_name': 'SYSTEM'}
DEBUG [sqlalchemy.engine.base.Engine] Col ('TABLE_NAME',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('ALEMBIC_VERSION',)
INFO  [sqlalchemy.engine.base.Engine] SELECT alembic_version.version_num 
FROM alembic_version
INFO  [sqlalchemy.engine.base.Engine] {}
DEBUG [sqlalchemy.engine.base.Engine] Col ('VERSION_NUM',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('34dacf7310ff',)
INFO  [sqlalchemy.engine.base.Engine] SELECT table_name FROM all_tables WHERE 
nvl(tablespace_name, 'no tablespace') NOT IN ('SYSTEM', 'SYSAUX') AND OWNER = 
:owner AND IOT_NAME IS NULL AND DURATION IS NULL
INFO  [sqlalchemy.engine.base.Engine] {'owner': 'SYSTEM'}
DEBUG [sqlalchemy.engine.base.Engine] Col ('TABLE_NAME',)
INFO  [alembic.autogenerate.compare] Detected added table 'dut_departments'
INFO  [alembic.autogenerate.compare] Detected added table 'dut_field_types'
INFO  [alembic.autogenerate.compare] Detected added table 'dut_uploadslog'
INFO  [alembic.autogenerate.compare] Detected added table 'dut_tables_info'
INFO  [alembic.autogenerate.compare] Detected added table 'dut_fields'
  Generating 
/Users/okyere/Repos/data_upload_sqlite/migrations/versions/08f3a17d96bb_.py ... 
done
(sqliteenv)Nanas-MacBook-Pro:data_upload_sqlite okyere$ python manage.py db 
upgrade
INFO  [sqlalchemy.engine.base.Engine] SELECT USER FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
DEBUG [sqlalchemy.engine.base.Engine] Col ('USER',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('SYSTEM',)
INFO  [sqlalchemy.engine.base.Engine] SELECT CAST('test plain returns' AS 
VARCHAR(60 CHAR)) AS anon_1 FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] SELECT CAST('test unicode returns' AS 
NVARCHAR2(60)) AS anon_1 FROM DUAL
INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [alembic.runtime.migration] Context impl OracleImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
INFO  [sqlalchemy.engine.base.Engine] SELECT table_name FROM all_tables WHERE 
table_name = :name AND owner = :schema_name
INFO  [sqlalchemy.engine.base.Engine] {'name': 'ALEMBIC_VERSION', 
'schema_name': 'SYSTEM'}
DEBUG [sqlalchemy.engine.base.Engine] Col ('TABLE_NAME',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('ALEMBIC_VERSION',)
INFO  [sqlalchemy.engine.base.Engine] SELECT alembic_version.version_num 
FROM alembic_version
INFO  [sqlalchemy.engine.base.Engine] {}
DEBUG [sqlalchemy.engine.base.Engine] Col ('VERSION_NUM',)
DEBUG [sqlalchemy.engine.base.Engine] Row ('34dacf7310ff',)
INFO  [alembic.runtime.migration] Running upgrade 34dacf7310ff -> 08f3a17d96bb, 
empty message
INFO  [sqlalchemy.engine.base.Engine] 
CREATE TABLE dut_departments (
        id INTEGER NOT NULL, 
        name VARCHAR2(120 CHAR) NOT NULL, 
        PRIMARY KEY (id), 
        UNIQUE (name)
)


INFO  [sqlalchemy.engine.base.Engine] {}
INFO  [sqlalchemy.engine.base.Engine] ROLLBACK
Traceback (most recent call last):
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/engine/base.py",
 line 1139, in _execute_context
    context)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/engine/default.py",
 line 450, in do_execute
    cursor.execute(statement, parameters)
cx_Oracle.DatabaseError: ORA-00955: name is already used by an existing object


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "manage.py", line 16, in <module>
    manager.run()
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/flask_script/__init__.py",
 line 412, in run
    result = self.handle(sys.argv[0], sys.argv[1:])
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/flask_script/__init__.py",
 line 383, in handle
    res = handle(*args, **config)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/flask_script/commands.py",
 line 216, in __call__
    return self.run(*args, **kwargs)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/flask_migrate/__init__.py",
 line 233, in upgrade
    command.upgrade(config, revision, sql=sql, tag=tag)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/command.py",
 line 174, in upgrade
    script.run_env()
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/script/base.py",
 line 397, in run_env
    util.load_python_file(self.dir, 'env.py')
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/util/pyfiles.py",
 line 81, in load_python_file
    module = load_module_py(module_id, path)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/util/compat.py",
 line 68, in load_module_py
    module_id, path).load_module(module_id)
  File "<frozen importlib._bootstrap>", line 539, in _check_name_wrapper
  File "<frozen importlib._bootstrap>", line 1614, in load_module
  File "<frozen importlib._bootstrap>", line 596, in _load_module_shim
  File "<frozen importlib._bootstrap>", line 1220, in load
  File "<frozen importlib._bootstrap>", line 1200, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1129, in _exec
  File "<frozen importlib._bootstrap>", line 1471, in exec_module
  File "<frozen importlib._bootstrap>", line 321, in _call_with_frames_removed
  File "migrations/env.py", line 87, in <module>
    run_migrations_online()
  File "migrations/env.py", line 80, in run_migrations_online
    context.run_migrations()
  File "<string>", line 8, in run_migrations
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/runtime/environment.py",
 line 797, in run_migrations
    self.get_context().run_migrations(**kw)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/runtime/migration.py",
 line 312, in run_migrations
    step.migration_fn(**kw)
  File 
"/Users/okyere/Repos/data_upload_sqlite/migrations/versions/08f3a17d96bb_.py", 
line 23, in upgrade
    sa.UniqueConstraint('name')
  File "<string>", line 8, in create_table
  File "<string>", line 3, in create_table
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/operations/ops.py",
 line 1098, in create_table
    return operations.invoke(op)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/operations/base.py",
 line 318, in invoke
    return fn(self, operation)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/operations/toimpl.py",
 line 101, in create_table
    operations.impl.create_table(table)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/ddl/impl.py",
 line 194, in create_table
    self._exec(schema.CreateTable(table))
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/ddl/oracle.py",
 line 22, in _exec
    result = super(OracleImpl, self)._exec(construct, *args, **kw)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/alembic/ddl/impl.py",
 line 118, in _exec
    return conn.execute(construct, *multiparams, **params)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/engine/base.py",
 line 914, in execute
    return meth(self, multiparams, params)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/sql/ddl.py",
 line 68, in _execute_on_connection
    return connection._execute_ddl(self, multiparams, params)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/engine/base.py",
 line 968, in _execute_ddl
    compiled
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/engine/base.py",
 line 1146, in _execute_context
    context)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/engine/base.py",
 line 1341, in _handle_dbapi_exception
    exc_info
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/util/compat.py",
 line 189, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=exc_value)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/util/compat.py",
 line 182, in reraise
    raise value.with_traceback(tb)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/engine/base.py",
 line 1139, in _execute_context
    context)
  File 
"/Users/okyere/miniconda3/envs/sqliteenv/lib/python3.4/site-packages/sqlalchemy/engine/default.py",
 line 450, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.DatabaseError: (cx_Oracle.DatabaseError) ORA-00955: name is 
already used by an existing object
 [SQL: '\nCREATE TABLE dut_departments (\n\tid INTEGER NOT NULL, \n\tname 
VARCHAR2(120 CHAR) NOT NULL, \n\tPRIMARY KEY (id), \n\tUNIQUE (name)\n)\n\n']

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