I'm not sure whether this is the cause of your problem, but I've seen similar errors and (other strange behavior) if you try to import movies / micrographs into Relion using relative paths... e.g. something like ../somewhereElse/Movies/*.tiff. Relion really likes the Movie / Micrographs directory to be within the project directory, ideally something like Movies/*.tiff. Even if the original files are located elsewhere, you can satisfy this by creating a symbolic link from the original location to Movies in the project dir.
Hope this helps.
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