I'm trying to use rtracklayer to run a liftOver. I have the GFF file as well as the fasta file for my reference genome. I'm not able to make lifOver work. It runs, but no sequence match: 

library(rtracklayer)
ch = import.chain("~/Desktop/LiftOver test/geoFor1ToTaeGut1.over.chain")

    Warning message:
    In if (is.null(value)) { :
      closing unused connection 3 (~/Desktop/LiftOver test/geoFor1ToTaeGut1.over.chain)

gff.mgf = import.gff3(con = "~/Desktop/LiftOver test/ref_GeoFor_1.0_top_level.gff3")
liftOver(x = gff.mgf,
         chain = ch)

Discarding unchained sequences: NW_005054297.1, NW_005054298.1, NW_005054299.1, NW_005054300.1, NW_005054301.1, NW_005054302.1, NW_005054303.1, NW_005054304.1, NW_005054305.1, NW_005054306.1, NW_005054307.1, NW_005054308.1, NW_005054309.1, NW_005054310.1, NW_005054311.1, NW_005054312.1, NW_005054313.1, NW_005054314.1, NW_005054315.1, NW_005054316.1, NW_005054317.1, NW_005054318.1, NW_005054319.1, NW_005054320.1, NW_005054321.1, NW_005054322.1, NW_005054323.1, NW_005054324.1, NW_005054325.1, NW_005054326.1, NW_005054327.1, NW_005054328.1, NW_005054329.1, NW_005054330.1, NW_005054331.1, NW_005054332.1, NW_005054333.1, NW_005054334.1, NW_005054335.1, NW_005054336.1, NW_005054337.1, NW_005054338.1, NW_005054339.1, NW_005054340.1, NW_005054341.1, NW_005054342.1, NW_005054343.1, NW_005054344.1, NW_005054345.1, NW_005054346.1, NW_005054347.1, NW_005054348.1, NW_005054349.1, NW_005054350.1, NW_005054351.1, NW_005054352.1, NW_005054353.1, NW_005054354.1, NW_005054355.1, NW_005054356.1, NW_00505... <truncated>GRangesList object of length 457437:
[[1]] 
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>

[[2]] ...

Is there a way to run liftOver using a GFF file or a reference genome? 

In the help documentation: 

x => The intervals to lift-over, usually a GRanges.

How do you create this GRanges object and from which file? A fasta? A GFF? 

The ranges to lift over are coming from the GFF file, so that should be the GRanges, and that's what import() gives you. The sequence names in the GFF file have to match the names in the chain file. My guess is that you either need to rename the sequences in the GRanges or maybe you don't even have the right chain file.