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Using du.exe to calculate disk usage on a Microsoft cluster server

I need to determine disk usage for each directory on a Microsoft cluster server. As a linux junkie, du is *the* tool for automating this kind of stuff so I installed cygwin, mapped some drives and tried to schedule the utility to run at night. However, I get a lot of errors thrown back such as:
1. "No such file or directory" - Which tends to appear on weird filenames (like with spaces or ' or some other character) or when I don't have permission to access the drive (but that's something I can fix)
2. "File name too long" - Which it is, but I'd hope there is some way to get around this
3. "du: fts_read failed: Permission denied" - That's the last error message I get. The program seems to crash at this point.

I've seen no such issue in Linux and Google responses to the third error are rare and unhelpful.

My question to the list is:
1. Is there a way to eliminate the errors above (especially the third so it can at least complete)
2. Has anyone else found a solution which will properly report the amount of disk space a particular directory is occupying? Something that is free and can be scheduled to run at night.

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