why CLIPPER only generates rep1 and rep2?

[FionaMoon]

Hi eCLIP group,
I run eclip pipeline calls enriched peak regions (peak clusters) with CLIPPER.
I finally got bed file like this

Only 2 replicates in the output file.

I have 3 experiment data and 3 controls. I merged 3 experiment data with samtools and I expected to get 3 replicates in output files.

Could you give me some advise to solve this problem?
Thank you in advance.

[byee4]

If more than one entry has the same name, final outputs from those entries might override each other. Check if that might be the case here

[FionaMoon]

I've tried to rename these bam files and merged them as the input of Clipper.
I found no matter how many bam files I merged, the output of clipper would always have 2 replicates.

I also see another answer which said clipper can only dual with 2 replicates so it's better to use skipper.

Is that true? What should I do If I have multiple replicates and want to perform peak calling and normalization?