I used the cnv_facets package to obtain CNV between normal and diseased for cattle. I got the Fasta and VCF files from Ensemble. Each FASTQ file is about 2 GB in size, my data is whole genome. But in the output of the Excel file, I see only one chromosome. I run the following command:

cnv_facets.R -t 234h.sorted.bam -n 475.sorted.bam -vcf bos_taurus.vcf.gz -o output_prefi

Thank you for your guidance