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In recent years, the gap between theory and practice in quantum key distribution (QKD) has been significantly narrowed, particularly for QKD systems with arbitrarily flawed optical receivers. The status for QKD systems with imperfect light sources is however less satisfactory, in the sense that the resulting secure key rates are often overly dependent on the quality of state preparation. This is especially the case when the channel loss is high. Very recently, to overcome this limitation, Tamaki et al proposed a QKD protocol based on the so-called ‘rejected data analysis’, and showed that its security—in the limit of infinitely long keys—is almost independent of any encoding flaw in the qubit space, being this protocol compatible with the decoy state method. Here, as a step towards practical QKD, we show that a similar conclusion is reached in the finite-key regime, even when the intensity of the light source is unstable. More concretely, we derive security bounds for a wide class of realistic light sources and show that the bounds are also efficient in the presence of high channel loss. Our results strongly suggest the feasibility of long distance provably secure communication with imperfect light sources.