This is a warning, not an error I suppose! From a quick Internet search, I found this warning means that some of the weights in the pretrained checkpoint, bert-based-uncased, will not be used for BERTForSequenceClassification. Some weights will be discarded. So TLDR, you can disregard the message and train the sequence classification model without any problems.

Check this link for more detailed explanation: https://github.com/huggingface/transformers/issues/5421