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nygenome / Conpair

Concordance and contamination estimator for tumor–normal pairs
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estimate_tumor_normal_contamination.py: ValueError: Not a bracketing interval. #3

Closed iranmdl closed 7 years ago

iranmdl commented 7 years ago

Hello, I'm having the following error when trying to estimate the contamination in my samples: This is my command:

/shared/tools/src/Conpair/.env/bin/python /shared/tools/src/Conpair/scripts/estimate_tumor_normal_contamination.py  -T tumor.pileup -N normal.pileup -Q 1
Normal sample contamination level: 2.774%

And this is the error:

Traceback (most recent call last):
  File "/shared/tools/src/Conpair/scripts/estimate_tumor_normal_contamination.py", line 215, in <module>
    optimal_val = ContaminationModel.apply_brents_algorithm(Data, Scores, (x1, x2, x3))
  File "/shared/tools/src/Conpair/modules/ContaminationModel.py", line 114, in apply_brents_algorithm
    optimal_val = scipy.optimize.brent(f, brack=(x1, x2, x3), tol=1.0e-07, maxiter=30)
  File "/shared/tools/src/Conpair/.env/local/lib/python2.7/site-packages/scipy/optimize/optimize.py", line 2003, in brent
    res = _minimize_scalar_brent(func, brack, args, **options)
  File "/shared/tools/src/Conpair/.env/local/lib/python2.7/site-packages/scipy/optimize/optimize.py", line 2035, in _minimize_scalar_brent
    brent.optimize()
  File "/shared/tools/src/Conpair/.env/local/lib/python2.7/site-packages/scipy/optimize/optimize.py", line 1841, in optimize
    xa, xb, xc, fa, fb, fc, funcalls = self.get_bracket_info()
  File "/shared/tools/src/Conpair/.env/local/lib/python2.7/site-packages/scipy/optimize/optimize.py", line 1829, in get_bracket_info
    raise ValueError("Not a bracketing interval.")
ValueError: Not a bracketing interval.
ewabergmann commented 7 years ago

Hi iranmdl,

I apologize for a very late response (I am currently on maternity leave). If you are still interested in solving the issue, would you mind sharing the tumor and normal pileup files?

Thank you for reporting the issue!