No output from HATK.py --hla2hped

[jinghuazhao]

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

[WansonChoi]

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 Jinghua, Have you solved that problem? I encountered the same issue.