[BUG]AttributeError: 'NoneType' object has no attribute 'scatter'

[brianpenghe]

I was running this command:

%%time
adjacencies = grnboost2(ex_matrix, tf_names=tf_names,verbose=True,client_or_address=custom_client)

And then I got this error:
preparing dask client
parsing input
creating dask graph
not shutting down client, client was created externally
finished
/usr/local/lib/python3.6/dist-packages/arboreto/algo.py:214: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.
expression_matrix = expression_data.as_matrix()

AttributeError Traceback (most recent call last)
in

/usr/local/lib/python3.6/dist-packages/arboreto/algo.py in grnboost2(expression_data, gene_names, tf_names, client_or_address, early_stop_window_length, limit, seed, verbose)
39 return diy(expression_data=expression_data, regressor_type='GBM', regressor_kwargs=SGBM_KWARGS,
40 gene_names=gene_names, tf_names=tf_names, client_or_address=client_or_address,
---> 41 early_stop_window_length=early_stop_window_length, limit=limit, seed=seed, verbose=verbose)
42
43

/usr/local/lib/python3.6/dist-packages/arboreto/algo.py in diy(expression_data, regressor_type, regressor_kwargs, gene_names, tf_names, client_or_address, early_stop_window_length, limit, seed, verbose)
126 early_stop_window_length=early_stop_window_length,
127 limit=limit,
--> 128 seed=seed)
129
130 if verbose:

/usr/local/lib/python3.6/dist-packages/arboreto/core.py in create_graph(expression_matrix, gene_names, tf_names, regressor_type, regressor_kwargs, client, target_genes, limit, include_meta, early_stop_window_length, repartition_multiplier, seed)
401 tf_matrix, tf_matrix_gene_names = to_tf_matrix(expression_matrix, gene_names, tf_names)
402
--> 403 future_tf_matrix = client.scatter(tf_matrix, broadcast=True)
404 # [1] wrap in a list of 1 -> unsure why but Matt. Rocklin does this often...
405 [future_tf_matrix_gene_names] = client.scatter([tf_matrix_gene_names], broadcast=True)

/usr/local/lib/python3.6/dist-packages/distributed/client.py in scatter(self, data, workers, broadcast, direct, hash, maxsize, timeout, asynchronous)
1873 broadcast=broadcast, direct=direct,
1874 local_worker=local_worker, timeout=timeout,
-> 1875 asynchronous=asynchronous, hash=hash)
1876
1877 @gen.coroutine

/usr/local/lib/python3.6/dist-packages/distributed/client.py in sync(self, func, *args, **kwargs)
674 return future
675 else:
--> 676 return sync(self.loop, func, *args, **kwargs)
677
678 def repr(self):

/usr/local/lib/python3.6/dist-packages/distributed/utils.py in sync(loop, func, *args, **kwargs)
280 e.wait(10)
281 if error[0]:
--> 282 six.reraise(*error[0])
283 else:
284 return result[0]

~/.local/lib/python3.6/site-packages/six.py in reraise(tp, value, tb)
701 if value.traceback is not tb:
702 raise value.with_traceback(tb)
--> 703 raise value
704 finally:
705 value = None

/usr/local/lib/python3.6/dist-packages/distributed/utils.py in f()
265 if timeout is not None:
266 future = gen.with_timeout(timedelta(seconds=timeout), future)
--> 267 result[0] = yield future
268 except Exception as exc:
269 error[0] = sys.exc_info()

/usr/local/lib/python3.6/dist-packages/tornado/gen.py in run(self)
727
728 try:
--> 729 value = future.result()
730 except Exception:
731 exc_info = sys.exc_info()

/usr/local/lib/python3.6/dist-packages/tornado/gen.py in wrapper(*args, **kwargs)
207 # performance penalty for the synchronous case.
208 try:
--> 209 yielded = next(result)
210 except (StopIteration, Return) as e:
211 future_set_result_unless_cancelled(

/usr/local/lib/python3.6/dist-packages/distributed/client.py in _scatter(self, data, workers, broadcast, direct, local_worker, timeout, hash)
1732 client=self.id)
1733 else:
-> 1734 yield self.scheduler.scatter(data=data2, workers=workers,
1735 client=self.id,
1736 broadcast=broadcast,

AttributeError: 'NoneType' object has no attribute 'scatter'

I was using desk 1.0.0 and pandas 0.23.4

Any thoughts?

[cflerin]

Please take a look at #163 and see if any of the suggestions there help to solve your problem.

[cflerin]

Please try with pySCENIC 0.11.0 to see if this resolves the issue.