Hi Jan and Myunghwa,
I recently encountered the same issue, while executing a clip on a Road Network Layer for France.
I use an ESRI Tool, (Data Management --> Clip).
Error report is as follows:
ExecuteError: ERROR 999999: Error executing function.
Invalid Topology [Negative point valence.]
Failed to execute (Clip).
My dataset is the entire Road Network of Europe, geoproccessed per Country, and for large Countries such as France or Germany, seperated in several partitions. The Road Network is in-turn separated in many classes, and I am almost sure it's not a memory issue.
Thank you in advance
Sergios