"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?

[Hu-JIN]

I recently ran into the same issue. In my case, the issue was caused by degeneracies in the signature matrix W. This happened when the supplied number of signatures is too large, resulting in at least 2 discovered de novo signatures being very similar. As a result, the de novo signature matrix W is not full rank, which leads to the non-convergence of nnls when solving for H.

So, my suggestion would be to reduce the number of signatures.