This may not be relevant as I am not familiar with what query does, but due to the way file buffering and access generally works the time spent doing the file access will usually show up as the fclose line as it does the heavy work there.
So when I have run profile in the past my e.g. fread instruction takes next to no time, but fclose takes a surprisingly long time. In my case it was really the file reading that took the time, it is just that the time taken to do this is assigned to the fclose line of code.
I'm sure there are others with far more expertise in the details of file buffering though and when work actually happens on different file access instructions.
