WansonChoi
commented
2 years ago Hi, @jinghuazhao. Thank you for using HATK and this error report.
I think the dimension of your HIBAG input data(4 columns) is different from that of the one(7 columns) that I described in the HLA2HPED README file((2) 'Usage Examples.' - 2. 'HIBAG'; https://github.com/WansonChoi/HATK/blob/master/docs/_0_HLA2HPED.md#2-usage-examples).
You can find more specific HIBAG example input data to the HLA2HPED here(https://github.com/WansonChoi/HATK/tree/master/example/HLA2HPED/HIBAG).
I think you should preprocess your input so that they are in the described format first, then give them as input to the HLA2HPED.
If another error occurs though you preprocessed your input or you need help for the preprocessing, let me know.
JingjingBai2021
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