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You didn't include the name of the client or the endpoint you're using, but from the format of the configuration and the options you're sending, it looks like you're using curl to call /2/files/upload to upload a file. The /2/files/upload endpoint is a "content-upload" style endpoint, meaning that it takes the file data in the request body.
With the curl code you're running here, you set the request body via the "--data-binary" option. You're passing "@$file" to that option which would tell curl to upload the contents of the local file at whatever path is in "$file". You'll need to check that "$file" contains the right value, and that the local file identified contains the expected non-empty data.