Deploying an end-to-end automatic speech recognition (ASR) model on mobile/embedded devices is a challenging task, since the device computational power and energy consumption requirements are dynamically changed in practice. To overcome the issue, we present a training and pruning method for ASR based on the connectionist temporal classification (CTC) which allows reduction of model depth at run-time without any extra fine-tuning. To achieve the goal, we adopt two regularization methods, intermediate CTC and stochastic depth, to train a model whose performance does not degrade much after pruning. We present an in-depth analysis of layer behaviors using singular vector canonical correlation analysis (SVCCA), and efficient strategies for finding layers which are safe to prune. Using the proposed method, we show that a Transformer-CTC model can be pruned in various depth on demand, improving real-time factor from 0.005 to 0.002 on GPU, while each pruned sub-model maintains the accuracy of individually trained model of the same depth.