I want to convert the gtf file (gencode gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz) to genepred format. However, by using the UCSC gtfToGenepred executable, I had errors like this:

gunzip -c gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz |gtfToGenePred stdin test2.gpd
no exons defined for group ENSG00000223972.4, feature gene (perhaps try -ignoreGroupsWithoutExons)

I tried -ignoreGroupsWithoutExons. It worked but missed genes like -ignoreGroupsWithoutExons. Is there any general solution for this?

Thanks