Does anyone make your own gtf file?

[awenxu]

Hello, everyone.

I'm working with RNA-seq data from a organism that the genome sequencing is not completely finished.
I can finish the procedure from TopHat to Cufflinks without a gtf file. But when I finished cuffdiff, the cds.* files (e.g. cds.diff) is empty. so when I run "cummeRund".
So I try to make my own annotated gtf file accoring to the cufflinks results, and it seems that it can run with cufflinks, cuffmerge, cuffcompare, and cuffdiff. But still, the cds.* file is empty. and I checked the result of cufflinks, cuffmerge, cuffcompare, and cuffdiff. I could not find any record include the information from my own gtf file.
here is some lines of my own gtf file:
chrC GenBank gene 54005 62002 7997 + . gene_id 'QBC1'; transcript_id 'QBC1'
chrC GenBank mRNA 54005 62002 7997 + . gene_id 'QBC1'; transcript_id 'QBC1-A'
chrC GenBank mRNA 54505 62002 7497 + . gene_id 'QBC1'; transcript_id 'QBC1-B'
chrC GenBank CDS 54657 62388 7731 + . gene_id 'QBC1'; transcript_id 'QBC1-A'

My questions is what happened to my gtf file, does anybody make your own gtf file?

Any advices are appreciated!