Consider for example the libre software LAMMPS, which uses GNU General Public License. The user writes an input file. Then the software performs some calculations based on the instructions in the input file and produces an output file in simple text format. Now I would like to know what determines the license of the output file and who is the copyright holder of it.
If the output is a straightforward transformation of the input, then the copyright belongs to whoever holds the copyright on the input, as Dale M says.
In that case, if the user has licensed the input file under some permissive license, then the output will be under the same license.
But if the program applies random factors, or if there is interactive input from the user during the course of the program, or takes into account environmental factors so that the output is different for different runs of the same input file, the copyright on the output will belong to the user who runs the program. It may also be a derivative work of the input file, and require the permission of whoever holds the copyright on the input. If the input file was licensed under a permissive license tht allows creation of modified version, then such permission has been granted, but the user may need to put the output under a compatible license if the user releases the output at all.