If the file is on a partition other than the startup volume, it will not be in
~/.Trash/, rather it will be in
volumeName is the name of the partition and
userID is your user's numerical user ID (probably 501 if you only have one user).
To be certain you have the correct path to the file, I would recommend using Terminal's drag and drop feature. This also helps to avoid accidentally deleting files with the potentially dangerous
sudo rm -Rf command.
Without pressing return at the end, type
sudo rm -Rf with a trailing space at the end,
sudo rm -Rf <--leave a space after -Rf, do not press return yet
then drag the file you want to delete from the Finder into the Terminal window. Then press return.
If it still won't delete, you should probably verify the disk with Disk Utility.