replicates not pooled

[acgtcoder]

Thank you for making this pipeline available!
I am trying to use it to re-analyse a published MNase-seq data set. There are two groups, KO vs WT, and each has two replicates. The sequences are from SOLiD platform, single-ends, and read length is 50 bp. Here is my design file:

group,replicate,fastq_1,fastq_2
WT,1,/data/wt_mnase_rep1.fastq.gz,
WT,2,/data/wt_mnase_rep2.fastq.gz,
KO,1,/data/ebx_mnase_rep1.fastq.gz,
KO,2,/data/ebx_mnase_rep2.fastq.gz,

The pipeline finished w/o no incidents, but it didn't produce pooled results. Instead, each replicate has it's own results. Is it expected or I didn't set the run right?

Thank you,

-George