Hi Wanson, I found you again here.

I have generated HIBAG files and ran --hla2hped without any output; what went wrong?

My data looks like these,

==> hla-A.txt <==
110000305926 02:01 11:01 0.998277964699688
110000305952 02:01 23:01 0.997446682971027
110000315493 02:01 11:01 0.996833309885227
110000315494 01:01 11:01 0.999356136108585
110000315495 02:01 68:02 0.996394523025291

==> hla-B.txt <==
110000305926 35:03 40:01 0.996483303028323
110000305952 35:03 44:03 0.996058170852897
110000315493 07:02 51:01 0.979973145549816
110000315494 27:05 51:01 0.983677536591212
110000315495 14:02 40:01 0.999931336465755

==> hla-C.txt <==
110000305926 03:04 04:01 0.99702800865108
110000305952 04:01 12:03 0.985706535681109
110000315493 07:02 15:02 0.935367053452714
110000315494 01:02 15:02 0.967046049719371
110000315495 03:04 08:02 0.998047222012632

==> hla-DPB1.txt <==
110000305926 03:01 04:02 0.869700079358216
110000305952 02:01 04:01 0.980975143080741
110000315493 04:01 04:02 0.985367413950808
110000315494 03:01 04:02 0.623031768002789
110000315495 02:01 03:01 0.860760310114792

==> hla-DQA1.txt <==
110000305926 04:01 05:05 0.987233037781869
110000305952 01:01 01:04 0.914401511385624
110000315493 01:01 01:02 0.998804976028461
110000315494 01:02 03:01 0.974585184074591
110000315495 01:02 05:05 0.999699261445796

==> hla-DQB1.txt <==
110000305926 03:01 04:02 0.995922293824256
110000305952 05:01 05:03 0.994635904701175
110000315493 05:01 06:02 0.988185754174626
110000315494 03:02 06:02 0.96797184191931
110000315495 03:01 06:04 0.998293649517587

==> hla-DRB1.txt <==
110000305926 08:01 12:01 0.965919411658699
110000305952 01:01 14:01 0.569009175748051
110000315493 01:01 15:01 0.99165993368937
110000315494 04:01 15:01 0.646629285820924
110000315495 13:02 13:03 0.99818493737721

python HATK.py
--hla2hped
--platform HIBAG
--out HLA/HIBAG/hla_HIBAG
--rhped
HLA/HIBAG/hla-A.txt
HLA/HIBAG/hla-B.txt
HLA/HIBAG/hla-C.txt
NA
HLA/HIBAG/hla-DPB1.txt
HLA/HIBAG/hla-DQA1.txt
HLA/HIBAG/hla-DQB1.txt
HLA/HIBAG/hla-DRB1.txt

with screen output
Namespace(Ggroup=False, HLA=None, NoCaption=False, Pgroup=False, aa=None, ar=None, bmarkergenerator=False, chped=None, condition=None, condition_list=None, covar=None, covar_name=None, dict_AA=None, dict_SNPS=None, fam=None, fourF=False, hat=None, heatmap=False, hg=None, hla2hped=True, hped=None, imgt=None, imgt2seq=False, imgt_dir=None, input=None, leave_NotFound=False, logistic=False, manhattan=False, maptable=None, metaanalysis=False, multiprocess=1, no_indel=False, nomencleaner=False, omnibus=False, oneF=False, out='/home/jhz22/Caprion/analysis/HLA/HIBAG/hla_HIBAG', phased=None, pheno=None, pheno_name=None, platform='HIBAG', point_color='#778899', point_size='15', reference_allele=None, rhped=['/home/jhz22/Caprion/analysis/HLA/HIBAG/hla-A.txt', '/home/jhz22/Caprion/analysis/HLA/HIBAG/hla-B.txt', '/home/jhz22/Caprion/analysis/HLA/HIBAG/hla-C.txt', 'NA', '/home/jhz22/Caprion/analysis/HLA/HIBAG/hla-DPB1.txt', '/home/jhz22/Caprion/analysis/HLA/HIBAG/hla-DQA1.txt', '/home/jhz22/Caprion/analysis/HLA/HIBAG/hla-DQB1.txt', '/home/jhz22/Caprion/analysis/HLA/HIBAG/hla-DRB1.txt'], s1_bim=None, s1_logistic_result=None, s2_bim=None, s2_logistic_result=None, save_intermediates=False, threeF=False, top_color='#FF0000', twoF=False, variants=None, yaxis_unit='10')

[HLA_Study.py]: HLA2HPED result :
HLA/HIBAG/hla_HIBAG.hped

head -5 HLA/HIBAG/hla_HIBAG.hped
110000305926 02:01 0 0 0 -9 0 0
110000305952 02:01 0 0 0 -9 0 0
110000315493 02:01 0 0 0 -9 0 0
110000315494 01:01 0 0 0 -9 0 0
110000315495 02:01 0 0 0 -9 0 0
...

Thank you!

JIng Hua