I got error on convert vcf step "Inconsistent marker IDs: [markers file]"

[NeiH4207]

[CookHLA.py]: CookHLA : Performing HLA imputation for 'MyHLAImputation/APMDA.samples.phased.COPY.LiftDown_hg18.NoAmbig'

• Java memory = 8000m(Mb)
• Using Local Embedding.
• Using Adaptive Genetic Map.
• Small Sample mode. (because # of target samples < 100)
  [1] Extracting SNPs from the MHC.
  [2] Performing SNP quality control.
  Warning: 3 variants had at least one non-A/C/G/T allele name.
  Warning: At least 2 duplicate IDs in --exclude file.
  62248
  62248
  62248
  [3] Converting data to beagle format.
  Exception in thread "main" java.lang.IllegalArgumentException: Inconsistent marker IDs: [markers file]=SNPS_DQA1_2481_32639939_intron1 [BEAGLE file]=chr6:32667088:G:A
  at beagleutil.Beagle2Vcf.checkConsistency(Beagle2Vcf.java:153)
  at beagleutil.Beagle2Vcf.main(Beagle2Vcf.java:67)

[HLA_Imputation.py::ERROR]: Input file for imputation('MyHLAImputation/APMDA.samples.51.MHC.QC.vcf') contains nothing. Please check it again.

[HLA_Imputation.py::ERROR]: Input file for imputation('MyHLAImputation/APMDA.samples.51.MHC.QC.vcf') contains nothing. Please check it again.

[HLA_Imputation.py::ERROR]: Input file for imputation('MyHLAImputation/APMDA.samples.51.MHC.QC.vcf') contains nothing. Please check it again.
....