I think you are getting this error since :
Your file is saved in a temporary location. When you are inside the callback function your file is removed from that location and you are getting "No such file" error. Path and other variables still exists as part of js and that's why you are able to print them in console.
Solution: Above(Outside) callback function move your file to some other permanent location using:
fs.rename(req.files.file.path, "./someKnownPath/filename");
Keep note of that location. In your callback function use the new location as path and try saving the file in gridfs. Once the file is saved you may delete it file from that location(/someKnownPath/filename).