Homozygous prediction for all samples

[yuanfeng719]

Hi,
I am trying to genotype my samples using Seq2HLA, but the results indicate all my samples are homozygous in all of the 3 MHC-I genes. Here is the output from one of the samples.

Command:
python $script/seq2HLA.py -2 BWA_reads_50M_AlleleSet10_1.fastq -1 BWA_reads_50M_AlleleSet10_2.fastq -r AlleleSet10_Seq2HLA

HLAgenotype2digits file:
#Locus Allele 1 Confidence Allele 2 Confidence
A A16 0.3422678 hoz("A10") 8.00000000023e-07
B B02 0 hoz("B02") NA
C C044 0.7426947 hoz("C011") 0.0056835

HLAgenotype4digits file:
#Locus Allele 1 Confidence Allele 2 Confidence
A A16:01 0.3422678 A16:01 8.00000000023e-07
B B02:3 0.0 B02:3 NA
C C044:01 0.7426947 C044:01 0.0056835

I am thinking maybe I didn't use it correctly. Do you notice anything wrong in my command?

Thanks,
Yuan