Is your dataset balanced (roughly as many positive as negative)?

Kernel SVMs as implemented in scikit-learn do not scale with the
number of samples: the computational cost is more than quadratic wrt
n_samples.
Either subsample (especially if you have a large imbalance), use an
approximation such as Nystroem [1] feature expansion + linear model or
use a more scalable non-linear algorithm such as
RandomForestsClassifier.

[1] http://scikit-learn.org/stable/modules/kernel_approximation.html

-- 
Olivier

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