Hi @Zeina,
The root of the error is here:
This can be caused by a variety of things- such as having a differing number of sequence counts, the sequences in one of the two paired files could be out of order with respect to the other, and/or there could be non standard headers in one or both of the files (causing the parser to "think" the files are mismatched).
Take a look at this related forum post, there are a few good suggestions for troubleshooting where the mismatch could be coming from. If you are still stuck, you can share your demux file and we can take a closer look.
Cheers 