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You have a bug in your print formatting which prints the y component twice.

 gndt_log_str = ('{0:.4f} {1:.4f} {1:.4f} {3:.4f} {4:.4f}'
                  ' {5:.4f} {6:.4f} {7:.4f}').format(time,
                  tx, ty, tz, qx, qy, qz, qw)