I had  3 samples (2replicates treated (A-B) and one untreated (C) ).

I did cufflnks and cuffmerge (all 3 cufflinks)

I run cuffdiff with the following options:
+ tophats from A, B, C (2 groups: gr.one with A, B), gropu2: C.

I had the following message:

0 bytes
An error occurred running this job: cuffdiff v1.3.0 (3022)
cuffdiff --no-update-check -q -p 8 -c 10 --FDR 0.050000 -N -b
/galaxy/data/hg19/sam_index/hg19.fa --labels +

Where did I do wrong? What does it mean?

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