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