"maximum number of iterations reached" in de novo signatures extraction

[Spirit-booze]

Hi.

Tried to use the package for de novo extraction of mutational signatures.

Got an error

RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/usr/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/home/spirit-booze/venvs/mut_signatures/lib/python3.10/site-packages/musical/mvnmf.py", line 406, in _job
model.fit()
File "/home/spirit-booze/venvs/mut_signatures/lib/python3.10/site-packages/musical/mvnmf.py", line 305, in fit
H = nnls(self.X, W)
File "/home/spirit-booze/venvs/mut_signatures/lib/python3.10/site-packages/musical/nnls.py", line 11, in nnls
h, _ = sp.optimize.nnls(W, x)
File "/home/spirit-booze/venvs/mut_signatures/lib/python3.10/site-packages/scipy/optimize/_nnls.py", line 93, in nnls
raise RuntimeError("Maximum number of iterations reached.")
RuntimeError: Maximum number of iterations reached.
"""

The above exception was the direct cause of the following exception:

RuntimeError Traceback (most recent call last)
Cell In[7], line 7
1 mut_sigs = musical.DenovoSig(mut_data,
2 min_n_components=1,
3 max_n_components=16,
4 ncpu=22,
5 verbose=2
6 )
----> 7 mut_sigs.fit()
9 with open('../temp_data/mut_results_01_11_2024.pkl', 'wb') as f:
10 pickle.dump(XPC_sigs, f)

File ~/venvs/mut_signatures/lib/python3.10/site-packages/musical/denovo.py:869, in DenovoSig.fit(self)
868 def fit(self):
--> 869 self._run_jobs()
870 self.postprocess()
871 return self

File ~/venvs/mut_signatures/lib/python3.10/site-packages/musical/denovo.py:750, in DenovoSig._run_jobs(self)
734 X_in = normalize(X_in, norm='l1', axis=0)
735 model = wrappedMVNMF(X_in,
736 n_components,
737 init=self.init,
(...)
748 noise=self.mvnmf_noise
749 )
--> 750 model.fit()
751 models = [model]
752 lambda_tilde = model.lambda_tilde

File ~/venvs/mut_signatures/lib/python3.10/site-packages/musical/mvnmf.py:443, in wrappedMVNMF.fit(self)
441 else:
442 workers = multiprocessing.Pool(self.ncpu)
--> 443 models = workers.map(self._job, list(self.lambda_tilde_grid))
444 workers.close()
445 workers.join()

File /usr/lib/python3.10/multiprocessing/pool.py:367, in Pool.map(self, func, iterable, chunksize)
362 def map(self, func, iterable, chunksize=None):
363 '''
364 Apply func to each element in iterable, collecting the results
365 in a list that is returned.
366 '''
--> 367 return self._map_async(func, iterable, mapstar, chunksize).get()

File /usr/lib/python3.10/multiprocessing/pool.py:774, in ApplyResult.get(self, timeout)
772 return self._value
773 else:
--> 774 raise self._value

RuntimeError: Maximum number of iterations reached.

Any ideas on how to resolve this?

[Hu-JIN]

Hi,

Someone else reported a similar error recently. We thought it may be related to this issue of a recent version of Scipy: scipy/scipy#20813. Could you check what version of Scipy you are using, and try downgrading it and run again?