At least 2 peak files (.BED) given by MACS2 have all the peaks of the file starting at position 0 even in different chromosomes.

This is an odd coincidence. Does any of you known of any reason (bad formatted input file or other) that could explain this?

The input SAM files have different starting positions.

Bellow is the script:

#!/bin/bash
TRT=/path/ChIP_FOS_CD49f.SAM
CTRL=/path/Input_FOS_CD49f.SAM
NAME=macs_chipvsinput_FOS_day2
macs2 -t $TRT\ 
-c $CTRL \ 
-g hs \
-n $NAME \
-f SAM \ 
-B \
-p 24