Most likely the input file to the tool contains a header line (the data was extracted from the UCSC table browser?). Certain tools do not accept this dataset formatting, even if the metadata is set to label certain rows as "Header lines".
So - Remove this track line header with the tool "Text manipulation -> Remove beginning of a file". (If you ever have a file with both a browser and a track line header, remove both). Then double check that the remainder of the file has consistent formatting (same number of columns for each row) if you have more problems. Tools like "Group" can help isolate where the problem is (which column), as the operations ("count" is the simplest) will present with errors if there are empty/missing columns.
Hopefully you solved the problem already or this helps, Jen, Galaxy team