Missing chr in gVCF

Hi,

I have generated a gVCF file using GATK-3.7 and it is completed without any error. However, i notice only few chromosome names in the first column of the gVCF file:

 java -Xmx10G -GenomeAnalysisTK.jar -R species.fa -T HaplotypeCaller -I Input.bam -stand_call_conf 30 -ERC GVCF --min_base_quality_score 20 --variant_index_parameter 128000 --variant_index_type LINEAR --genotyping_mode DISCOVERY -o GATK.g.vcf.gz

  less GATK.g.vcf.gz | grep -v "##" | cut -f1| sort | uniq
  chr1
  chr10
  chr11
  chr12
  chr13
 #CHROM

Does it mean that the run is incomplete? or ami i missing some property of gVCF format.