How are you specifying your parameters?
The presence of asterisks in the filename indicates to me that you might have a wildcard escaping issue. Rosetta itself doesn’t do any sort of wildcard expansion (or similar things like tilde expansion). It relies instead on the shell you’re using to do the expansion. As such, if you pass in a filename to Rosetta like “/**/general_FD.flags”, Rosetta expects there to be a directory off of the root directory with the literal name of “**” (two literal asterisks). If that’s supposed to be a shorthand for something, it’s the shell which is supposed to do the shorthand substitution.
This sort of thing happens most often when you move parameters into options files (Rosetta is the one reading the option file, and will not do the wildcard expansion), or when you add quotes to your commandline, and thus bypass your shell’s expansion proceedures.
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