I've got the scflow main quantnuclei pipeline to run. However the pipeline.log always ends with the following error message, regardless of what part of the pipeline was running. The outputs are all there as expected. I think it's possibly to do with the conda env?
Error from pipeline.log
`
Original exception:
Exception #1
'<class 'TypeError'>handle_sigint() got multiple values for argument 'pool'' raised in ...
Traceback (most recent call last):
File "/home/c/ccohen/conda/obds_conda/envs/scflow/lib/python3.8/site-packages/ruffus/task.py", line 5250, in pipeline_run
job_result = ii.next(**itr_kwargs)
File "src/gevent/_imap.py", line 105, in gevent._gevent_c_imap.IMapUnordered.next
File "src/gevent/_imap.py", line 113, in gevent._gevent_c_imap.IMapUnordered._inext
File "src/gevent/queue.py", line 350, in gevent._gevent_cqueue.Queue.get
File "src/gevent/queue.py", line 327, in gevent._gevent_cqueue.Queue._Queue__get_or_peek
File "src/gevent/_waiter.py", line 154, in gevent._gevent_c_waiter.Waiter.get
File "src/gevent/_greenlet_primitives.py", line 61, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
File "src/gevent/_greenlet_primitives.py", line 61, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
File "src/gevent/_greenlet_primitives.py", line 65, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
File "src/gevent/_gevent_c_greenlet_primitives.pxd", line 35, in gevent._gevent_c_greenlet_primitives._greenlet_switch
TypeError: handle_sigint() got multiple values for argument 'pool'
\
2023-03-10 08:58:50,243 ERROR main control - end of all error messages
`
Error from nohup.out
`Original exception:
Exception #1
'<class 'TypeError'>handle_sigint() got multiple values for argument 'pool'' raised in ...
Traceback (most recent call last):
File "/home/c/ccohen/conda/obds_conda/envs/scflow/lib/python3.8/site-packages/ruffus/task.py", line 5250, in pipeline_run
job_result = ii.next(**itr_kwargs)
File "src/gevent/_imap.py", line 105, in gevent._gevent_c_imap.IMapUnordered.__next__
File "src/gevent/_imap.py", line 113, in gevent._gevent_c_imap.IMapUnordered._inext
File "src/gevent/queue.py", line 350, in gevent._gevent_cqueue.Queue.get
File "src/gevent/queue.py", line 327, in gevent._gevent_cqueue.Queue._Queue__get_or_peek
File "src/gevent/_waiter.py", line 154, in gevent._gevent_c_waiter.Waiter.get
File "src/gevent/_greenlet_primitives.py", line 61, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
File "src/gevent/_greenlet_primitives.py", line 61, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
File "src/gevent/_greenlet_primitives.py", line 65, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
File "src/gevent/_gevent_c_greenlet_primitives.pxd", line 35, in gevent._gevent_c_greenlet_primitives._greenlet_switch
TypeError: handle_sigint() got multiple values for argument 'pool'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/c/ccohen/conda/obds_conda/envs/scflow/bin/scflow", line 33, in
sys.exit(load_entry_point('scflow', 'console_scripts', 'scflow')())
File "/ceph/project/tendonhca/ccohen/git/scflow/scpipelines/entry.py", line 104, in main
module.main(sys.argv)
File "/ceph/project/tendonhca/ccohen/git/scflow/scpipelines/pipeline_quantnuclei.py", line 269, in main
P.main(argv)
File "/home/c/ccohen/conda/obds_conda/envs/scflow/lib/python3.8/site-packages/cgatcore/pipeline/control.py", line 1528, in main
run_workflow(args)
File "/home/c/ccohen/conda/obds_conda/envs/scflow/lib/python3.8/site-packages/cgatcore/pipeline/control.py", line 1458, in run_workflow
raise ValueError("pipeline failed with errors") from ex
ValueError: pipeline failed with errors
`