why does cuffdiff discard some transcripts in GTF file

[liuxq]

I call cuffdiff using basic commands

cuffdiff Macaca_mulatta.MMUL_1.61.gtf s_4.bam s_5.bam -o output

I find in both isoforms.fpkm_tracking and isoform_exp.diff, some transcripts in gtf file are just discarded. Below is the gtf part for a discarded transcript having no fpkm compuation or differentally expression test.

chr14 protein_coding exon 2878936 2879770 . + . gene_id "ENSMMUG00000007746"; transcript_id "ENSMMUT00000044732"; exon_number "1";
chr14 protein_coding CDS 2879347 2879770 . + 0 gene_id "ENSMMUG00000007746"; transcript_id "ENSMMUT00000044732"; exon_number "1"; protein_id "ENSMMUP00000037750";
chr14 protein_coding start_codon 2879347 2879349 . + 0 gene_id "ENSMMUG00000007746"; transcript_id "ENSMMUT00000044732"; exon_number "1";
chr14 protein_coding exon 2880766 2881014 . + . gene_id "ENSMMUG00000007746"; transcript_id "ENSMMUT00000044732"; exon_number "2";
chr14 protein_coding CDS 2880766 2881001 . + 2 gene_id "ENSMMUG00000007746"; transcript_id "ENSMMUT00000044732"; exon_number "2"; protein_id "ENSMMUP00000037750";
chr14 protein_coding stop_codon 2881002 2881004 . + 0 gene_id "ENSMMUG00000007746"; transcript_id "ENSMMUT00000044732"; exon_number "2";