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Augustus error in test_data #277

Closed larryns closed 1 year ago

larryns commented 1 year ago

Hi,

I'm running the test_data set for cat and am getting the following errors:

INFO: 2023-01-03 20:15:55,740 - Launching homGeneMapping for augPB.
INFO: 2023-01-03 20:16:06,820 - Loaded table: hg38.augPB_Hgm
INFO: 2023-01-03 20:16:07,806 - [pid 89] Worker Worker(salt=5174978122, workers=1, host=48368e586417, username=lsingh, pid=89) done      Task: HgmDriverTask for augPB
INFO: 2023-01-03 20:16:07,812 - Informed scheduler that task   HgmDriverTask_False_True_True_d1496ef73e   has status   DONE
INFO: 2023-01-03 20:16:07,816 - [pid 89] Worker Worker(salt=5174978122, workers=1, host=48368e586417, username=lsingh, pid=89) running   ToilTask: AugustusDriverTask for canFam3 using batchSystem single_machine
ERROR: 2023-01-03 20:16:24,300 - Exception during reset or similar
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 412, in _make_request
    httplib_response = conn.getresponse(buffering=True)
TypeError: getresponse() got an unexpected keyword argument 'buffering'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/pool/base.py", line 757, in _finalize_fairy
    fairy._reset(pool, transaction_was_reset)
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/pool/base.py", line 1016, in _reset
    pool._dialect.do_rollback(self)
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/engine/default.py", line 683, in do_rollback
    dbapi_connection.rollback()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140140203337536 and this is thread id 140134534805248.
ERROR: 2023-01-03 20:16:24,302 - Exception closing connection <sqlite3.Connection object at 0x7f74e198c7b0>
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 412, in _make_request
    httplib_response = conn.getresponse(buffering=True)
TypeError: getresponse() got an unexpected keyword argument 'buffering'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/pool/base.py", line 757, in _finalize_fairy
    fairy._reset(pool, transaction_was_reset)
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/pool/base.py", line 1016, in _reset
    pool._dialect.do_rollback(self)
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/engine/default.py", line 683, in do_rollback
    dbapi_connection.rollback()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140140203337536 and this is thread id 140134534805248.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/pool/base.py", line 260, in _close_connection
    self._dialect.do_terminate(connection)
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/engine/default.py", line 689, in do_terminate
    self.do_close(dbapi_connection)
  File "/usr/local/lib/python3.8/dist-packages/sqlalchemy/engine/default.py", line 692, in do_close
    dbapi_connection.close()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140140203337536 and this is thread id 140134534805248.
ERROR: 2023-01-03 20:16:24,302 - Exception during reset or similar
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 412, in _make_request
    httplib_response = conn.getresponse(buffering=True)
TypeError: getresponse() got an unexpected keyword argument 'buffering'

During handling of the above exception, another exception occurred:

...

I'm using the local binary mode (not Docker) and installed the latest version of Augustus from source (github).

Any thoughts on what's causing this error and what I can do?

Thanks very much for any help. Larry.

larryns commented 1 year ago

It looks like upgrading toil from 5.0.0 to the latest 5.7.1 seems to have solved my problem for anyone who runs into this problem in the future.