cuffdiff problems: only got 3 records in the gene_exp.diff file

[twotwo]

Hi,
I set up a cuffdiff running. Here is my code:
cuffdiff -o /home/twotwo /home/twotwo/reference.gtf {samples from group1 separated by comma}{space}{samples from group2 separated by comma}

Then the log looks fine for the first hundreds lines, with some loci processing...
Here is the last part:

Performed 188097 isoform-level transcription difference tests
Performed 0 tss-level transcription difference tests
Performed 3 gene-level transcription difference tests
Performed 0 CDS-level transcription difference tests
Performed 0 splicing tests
Performed 0 promoter preference tests
Performing 0 relative CDS output tests
Writing isoform-level FPKM tracking
Writing TSS group-level FPKM tracking
Writing gene-level FPKM tracking
Writing CDS-level FPKM tracking
Writing isoform-level count tracking
Writing TSS group-level count tracking
Writing gene-level count tracking
Writing CDS-level count tracking
Writing isoform-level read group tracking
Writing TSS group-level read group tracking
Writing gene-level read group tracking
Writing CDS-level read group tracking
Writing read group info
Writing run info


The problem is: There should be 188097 probes for comparing. However, I only got 3 probes (3 rows) in the gene expression output. Any comments on that? very confused.