Question: Tornado.util.TimeoutError timed out after 20 s
0
gravatar for sidrah.maryam
6 months ago by
sidrah.maryam20 wrote:

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.

ADD COMMENTlink modified 6 months ago by GenoMax95k • written 6 months ago by sidrah.maryam20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1803 users visited in the last hour
_