What is the `table` parameter in the UCSU ldHgGene tool?
I stumbled across this issue after getting the same warning message from liftOver. By using the -out option of lgHgGene, the database parameter is ignored but must still be provided. The table parameter should be the second column from your GTF file. Note that you must also specify the -gtf option (otherwise it expects GFF format). In my case, the GTF file looks like:

chr1    mm10_knownGene  exon    3073253 3074322 0.000000        +       .       gene_id "ENSMUST00000193812.1"; transcript_id "ENSMUST00000193812.1";
chr1    mm10_knownGene  exon    3102016 3102125 0.000000        +       .       gene_id "ENSMUST00000082908.1"; transcript_id "ENSMUST00000082908.1";
chr1    mm10_knownGene  exon    3206523 3207317 0.000000        -       .       gene_id "ENSMUST00000159265.1"; transcript_id "ENSMUST00000159265.1";
chr1    mm10_knownGene  exon    3213439 3215632 0.000000        -       .       gene_id "ENSMUST00000159265.1"; transcript_id "ENSMUST00000159265.1";
chr1    mm10_knownGene  exon    3205901 3207317 0.000000        -       .       gene_id "ENSMUST00000162897.1"; transcript_id "ENSMUST00000162897.1";
chr1    mm10_knownGene  exon    3213609 3216344 0.000000        -       .       gene_id "ENSMUST00000162897.1"; transcript_id "ENSMUST00000162897.1";
...


By default, ldHgGene outputs a leading 'bin' column which won't work with liftOver; this can be avoided with the -nobin option. So my command was:

ldHgGene -gtf -nobin -out=mm10.GENCODE_VM20.gp ignored mm10_knownGene mm10.GENCODE_VM20.gtf


The resulting genePred output can be fed directly into liftOver -genePred:

ENSMUST00000193812.1    chr1    +       3073252 3074322 3074322 3074322 1       3073252,        3074322,
ENSMUST00000082908.1    chr1    +       3102015 3102125 3102125 3102125 1       3102015,        3102125,
ENSMUST00000162897.1    chr1    -       3205900 3216344 3216344 3216344 2       3205900,3213608,        3207317,3216344,
ENSMUST00000159265.1    chr1    -       3206522 3215632 3215632 3215632 2       3206522,3213438,        3207317,3215632,