Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 14876 did not have 13 elements

In your data file, the line number noted (probably the last line in the file) has an problem  -- remove the noted line and all blank lines after it.  The file should be OK after that.  (The line has an end of line, but the data is not as expected.)

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Cosinor:  Phi or Acrophase is is not correct, but Mesor and Amplitude are.

There are several possibilities:

• The reference time being used is not in the same time zone as the data time zone (this can happen if the reference time is in Daylight Savings Time and the data is not, or vice versa).
• When comparing your output to a periodogram, or another analysis that doesn't use time, the starting time for that analysis will be the time of the first data point.  The Cosinor doesn't always use the first data point as the reference time, but usually users midnight, intead.  When adjusted for, the Phi's will match.
• Chronobiology uses a negative degree measure with respect to the normal method.  Degrees should be between 0 and -360 degrees in Chronobiology.