Entering edit mode
4.3 years ago
sidrah.maryam
▴
50
Hey everyone! I am trying to run scenic protocol, for network regulatory inference.
The code command is
pyscenic grn --num_workers 20 --output adj.tsv --method grnboost2 filtered.loom hs_hgnc_tfs.txt
And I am getting the following error
/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 {}
2020-07-21 22:55:37,466 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.
2020-07-21 22:55:37,616 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks.
/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 {}
tornado.application - ERROR - Multiple exceptions in yield list
Traceback (most recent call last):
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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 "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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
Traceback (most recent call last):
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/bin/pyscenic", line 8, in <module>
sys.exit(main())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 421, in main
args.func(args)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 71, in find_adjacencies_command
client, shutdown_callback = _prepare_client(args.client_or_address, num_workers=args.num_workers)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/prune.py", line 63, in _prepare_client
threads_per_worker=1)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/deploy/local.py", line 218, in __init__
self.start(ip=ip, n_workers=n_workers)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/deploy/local.py", line 256, in start
self.sync(self._start, **kwargs)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/deploy/local.py", line 249, in sync
return sync(self.loop, func, *args, **kwargs)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/utils.py", line 331, in sync
six.reraise(*error[0])
File "/home/sidrah19220/.local/lib/python3.6/site-packages/six.py", line 693, in reraise
raise value
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/utils.py", line 316, in f
result[0] = yield future
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/deploy/local.py", line 284, in _start
yield [self._start_worker(**self.worker_kwargs) for i in range(n_workers)]
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 501, in callback
result_list.append(f.result())
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/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
Exception ignored in: <bound method="" LocalCluster.__del__="" of="" LocalCluster('tcp:="" 127.0.0.1:38723',="" workers="0," ncores="0)">
Traceback (most recent call last):
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/deploy/local.py", line 444, in __del__
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/deploy/local.py", line 385, in close
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/deploy/local.py", line 249, in sync
File "/home/sidrah19220/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/distributed/utils.py", line 326, in sync
**tornado.util.TimeoutError: timed out after 20 s.**
Please help and Please suggest the solution.
