Interpretation of CNVkit output

Question

[Samiah]

I ran "batch" command of CNVkit on my normal and tumor bam files. I got .cnn, .cnr and .cns files of tumor files, then I used gainloss command using .cnr and .cns files:

cnvkit.py gainloss tumor.cnr -s tumor.cns -t 0.05 > tumor_gainloss.txt

My tumor.cnr and tumor.cns files contain all chromosomes but in the output of "tumor_gainloss.txt", only chromosome 1 is reported. Now I am interested that why this happened. Have I done something wrong and how can I interpret the results? I am using CNVkit for the first time.