Dear SCENIC developers,
I was trying to follow the tutorial (except for skipping the Scanpy part) for the PBMC10k protocol.
But I got an error in the first grn step.
!pyscenic grn {f_loom_path_scenic} {f_tfs} -o adj.csv --num_workers 20
/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}
2020-01-24 14:09:44,508 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.
2020-01-24 14:09:44,534 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks.
/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}
Traceback (most recent call last):
File "", line 1, in
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 243, in main
fds = reduction.recvfds(s, MAXFDS_TO_SEND + 1)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/reduction.py", line 155, in recvfds
raise EOFError
EOFError
distributed.nanny - WARNING - Worker process 47169 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47167 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47165 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47163 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47161 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47160 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47168 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47166 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47162 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47171 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47170 was killed by unknown signal
distributed.nanny - WARNING - Worker process 47164 was killed by unknown signal
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Restarting worker
/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self._semlock = _multiprocessing.SemLock._rebuild(*state)
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
FileNotFoundError: [Errno 2] No such file or directory
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 261, in main
old_handlers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 297, in _serve_one
code = spawn._main(child_r)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 110, in setstate
self._semlock = _multiprocessing.SemLock._rebuild(*state)
FileNotFoundError: [Errno 2] No such file or directory
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 306, in _start_worker
**kwargs
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/asyncio/tasks.py", line 630, in _wrap_awaitable
return (yield from awaitable.await())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 196, in _start
response = yield self.instantiate()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 276, in instantiate
timedelta(seconds=self.death_timeout), self.process.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 439, in start
yield self.process.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/process.py", line 35, in _call_and_set_future
res = func(*args, **kwargs)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/process.py", line 192, in _start
process.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 112, in start
self._popen = self._Popen(self)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/context.py", line 291, in _Popen
return Popen(process_obj)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/popen_forkserver.py", line 35, in init
super().init(process_obj)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init
self._launch(process_obj)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/popen_forkserver.py", line 51, in _launch
self.sentinel, w = forkserver.connect_to_new_process(self._fds)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/forkserver.py", line 70, in connect_to_new_process
child_r, parent_w = os.pipe()
OSError: [Errno 24] Too many open files
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 306, in _start_worker
**kwargs
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/asyncio/tasks.py", line 630, in _wrap_awaitable
return (yield from awaitable.await())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 196, in _start
response = yield self.instantiate()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 276, in instantiate
timedelta(seconds=self.death_timeout), self.process.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 416, in start
self.init_result_q = init_q = mp_context.Queue()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/context.py", line 102, in Queue
return Queue(maxsize, ctx=self.get_context())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/queues.py", line 41, in init
self._reader, self._writer = connection.Pipe(duplex=False)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/connection.py", line 517, in Pipe
fd1, fd2 = os.pipe()
OSError: [Errno 24] Too many open files
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 306, in _start_worker
**kwargs
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/asyncio/tasks.py", line 630, in _wrap_awaitable
return (yield from awaitable.await())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 196, in _start
response = yield self.instantiate()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 276, in instantiate
timedelta(seconds=self.death_timeout), self.process.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 416, in start
self.init_result_q = init_q = mp_context.Queue()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/context.py", line 102, in Queue
return Queue(maxsize, ctx=self.get_context())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/queues.py", line 41, in init
self._reader, self._writer = connection.Pipe(duplex=False)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/multiprocessing/connection.py", line 517, in Pipe
fd1, fd2 = os.pipe()
OSError: [Errno 24] Too many open files
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 306, in _start_worker
**kwargs
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/asyncio/tasks.py", line 630, in _wrap_awaitable
return (yield from awaitable.await())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 184, in _start
listen_args=self.listen_args,
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/core.py", line 322, in listen
self.listener.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/comm/tcp.py", line 421, in start
self.port, address=self.ip, backlog=backlog
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/netutil.py", line 140, in bind_sockets
sock = socket.socket(af, socktype, proto)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/socket.py", line 151, in init
_socket.socket.init(self, family, type, proto, fileno)
OSError: [Errno 24] Too many open files
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 306, in _start_worker
**kwargs
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/asyncio/tasks.py", line 630, in _wrap_awaitable
return (yield from awaitable.await())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 184, in _start
listen_args=self.listen_args,
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/core.py", line 322, in listen
self.listener.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/comm/tcp.py", line 421, in start
self.port, address=self.ip, backlog=backlog
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/netutil.py", line 140, in bind_sockets
sock = socket.socket(af, socktype, proto)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/socket.py", line 151, in init
_socket.socket.init(self, family, type, proto, fileno)
OSError: [Errno 24] Too many open files
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 306, in _start_worker
**kwargs
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/asyncio/tasks.py", line 630, in _wrap_awaitable
return (yield from awaitable.await())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 184, in _start
listen_args=self.listen_args,
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/core.py", line 322, in listen
self.listener.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/comm/tcp.py", line 421, in start
self.port, address=self.ip, backlog=backlog
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/netutil.py", line 140, in bind_sockets
sock = socket.socket(af, socktype, proto)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/socket.py", line 151, in init
_socket.socket.init(self, family, type, proto, fileno)
OSError: [Errno 24] Too many open files
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 306, in _start_worker
**kwargs
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/asyncio/tasks.py", line 630, in _wrap_awaitable
return (yield from awaitable.await())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 184, in _start
listen_args=self.listen_args,
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/core.py", line 322, in listen
self.listener.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/comm/tcp.py", line 421, in start
self.port, address=self.ip, backlog=backlog
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/netutil.py", line 140, in bind_sockets
sock = socket.socket(af, socktype, proto)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/socket.py", line 151, in init
_socket.socket.init(self, family, type, proto, fileno)
OSError: [Errno 24] Too many open files
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 306, in _start_worker
**kwargs
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/asyncio/tasks.py", line 630, in _wrap_awaitable
return (yield from awaitable.await())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/nanny.py", line 184, in _start
listen_args=self.listen_args,
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/core.py", line 322, in listen
self.listener.start()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/comm/tcp.py", line 421, in start
self.port, address=self.ip, backlog=backlog
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/netutil.py", line 140, in bind_sockets
sock = socket.socket(af, socktype, proto)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/socket.py", line 151, in init
_socket.socket.init(self, family, type, proto, fileno)
OSError: [Errno 24] Too many open files
Traceback (most recent call last):
File "/Users/levylabmini2/opt/anaconda3/bin/pyscenic", line 10, in
sys.exit(main())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 408, in main
args.func(args)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 64, in find_adjacencies_command
client, shutdown_callback = _prepare_client(args.client_or_address, num_workers=args.num_workers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/pyscenic/prune.py", line 63, in _prepare_client
threads_per_worker=1)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 218, in init
self.start(ip=ip, n_workers=n_workers)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 256, in start
self.sync(self._start, **kwargs)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 249, in sync
return sync(self.loop, func, *args, **kwargs)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/utils.py", line 331, in sync
six.reraise(*error[0])
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/six.py", line 693, in reraise
raise value
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/utils.py", line 316, in f
result[0] = yield future
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 284, in _start
yield [self._start_worker(**self.worker_kwargs) for i in range(n_workers)]
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/levylabmini2/opt/anaconda3/lib/python3.7/site-packages/distributed/deploy/local.py", line 316, in _start_worker
raise gen.TimeoutError("Worker failed to start")
tornado.util.TimeoutError: Worker failed to start