Hi I have ran the cuffdiff over my BAM files derived from Tophat but all the output files are empty and I did not receive any errors during running it. Do you have any ideas where is the mistake? Thanks a lot in advance.

#!/bin/bash
#$ -cwd
#$ -pe smp 12
module use /app/modulefiles
module add samtools
module add bowtie/0.12.7
module add tophat/1.4.0
module add cufflinks/2.0.2-beta

cuffdiff -o cuffdiff_output_merged -p 12 -G /Annotation/genes.gtf -u -L brain,liver/brain_1/accepted_hits.bam,/brain_2/accepted_hits.bam,/brain_3/accepted_hits.bam,/brain_4/accepted_hits.bam /liver_1/accepted_hits.bam,/liver_2/accepted_hits.bam,/liver_3/accepted_hits.bam,/liver_4/accepted_hits.bam