No variants for bmarkergenerator

[uedaMT]

Hi,

I am analyzing my SNPs from hg19 using your tool. But I got errors when I was running the bmarkergenerator (and no output).
Here is the error I got.

#///////////////////////////
Error: No variants remaining after --exclude.
Error: No variants remaining after --exclude.
Error: Failed to open MybMarkerGenerator/exp_hla-typ_GEUV.hg19.SNPS.CODED.bed.
Error: Failed to open MybMarkerGenerator/exp_hla-typ_GEUV.hg19.AA.CODED.bed.
rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.SNPS.CODED.bed' cannot remove: No such file or directory rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.SNPS.CODED.bim' cannot remove: No such file or directory
rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.SNPS.CODED.fam' cannot remove: No such file or directory rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.AA.CODED.bed' cannot remove: No such file or directory
rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.AA.CODED.bim' cannot remove: No such file or directory rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.AA.CODED.fam' cannot remove: No such file or directory
Error: Failed to open MybMarkerGenerator/exp_hla-typ_GEUV.hg19.AA.FOUNDERS.fam.
rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.AA.FOUNDERS.bed' cannot remove: No such file or directory rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.AA.FOUNDERS.bim' cannot remove: No such file or directory
rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.AA.FOUNDERS.fam' cannot remove: No such file or directory rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.SNPS.FOUNDERS.bed' cannot remove: No such file or directory
rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.SNPS.FOUNDERS.bim' cannot remove: No such file or directory rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.SNPS.FOUNDERS.fam' cannot remove: No such file or directory
Error: Failed to open MybMarkerGenerator/exp_hla-typ_GEUV.hg19.MERGED.bed.
awk: fatal: file MybMarkerGenerator/exp_hla-typ_GEUV.hg19.MERGED.FRQ.frq' Cannot open file for reading (No such file or directory ) awk: fatal: file MybMarkerGenerator/exp_hla-typ_GEUV.hg19.MERGED.FRQ.frq' Cannot open file for reading (No such file or directory )
Error: Failed to open MybMarkerGenerator/exp_hla-typ_GEUV.hg19.MERGED.bed.
Error: Failed to open MybMarkerGenerator/exp_hla-typ_GEUV.hg19.bed.
rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.MERGED.bed' cannot remove: No such file or directory rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.MERGED.bim' cannot remove: No such file or directory
rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.MERGED.fam' cannot remove: No such file or directory rm: MybMarkerGenerator/exp_hla-typ_GEUV.hg19.MERGED.FRQ.frq' cannot remove: No such file or directory
Namespace(Ggroup=False, HLA=None, NoCaption=False, Pgroup=False, aa=None, ar=None, bmarkergenerator=True, chped='MyNomenCleaner/exp_hla-typ_GEUV_hg19.2field.chped', condition=None, condition_list=None, covar=None, covar_name=None, dict_AA='MyIMGT2Seq/HLA_DICTIONARY_AA.hg19.imgt3320', dict_SNPS='MyIMGT2Seq/HLA_DICTIONARY_SNPS.hg19.imgt3320', fam=None, fourF=False, hat=None, heatmap=False, hg='19', hla2hped=False, 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='MybMarkerGenerator/exp_hla-typ_GEUV.hg19', phased=None, pheno=None, pheno_name=None, platform=None, point_color='#778899', point_size='15', reference_allele=None, rhped=None, 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')

[bMarkerGenerator.py]: Making Reference Panel for "MybMarkerGenerator/exp_hla-typ_GEUV.hg19"

[1] Generating Amino acid(AA)sequences from HLA types.
[2] Encoding Amino acids positions.
[3] Encoding HLA alleles.
[4] Generating DNA(SNPS) sequences from HLA types.
[5] Encoding SNP positions.
[6] Extracting founders.
[6] Merging SNP, HLA, and amino acid datasets.
[7] Performing quality control.
[8] Making reference panel for HLA-AA,SNPS,HLA is Done!

[HLA_Study.py]: bMarkerGenerator result(Prefix) :
MybMarkerGenerator/exp_hla-typ_GEUV.hg19
#///////////////////////////////////

The error said that no variants for generating marker panel?
No error occurred when I preprocessed IMGT-HLA database for hg19 (using provided one in "example/IMGTHLA3320"), generated hped file, and updated the nomenclature, and I obtained all the outputs which look OK...
I will appreciate if you kindly help me out to solve this problem.

Here are my Codes I used in the above analyses.

• preprocessed IMGT-HLA database
  python3 HATK.py \
  --imgt2seq \
  --hg 19 \
  --imgt 3320 \
  --out MyIMGT2Seq/ExamplePrefix.hg19.imgt3320 \
  --imgt-dir example/IMGTHLA3320 \
  --multiprocess 8

• Nomenclature
  python3 HATK.py \
  --nomencleaner \
  --hat MyIMGT2Seq/HLA_ALLELE_TABLE.imgt3320.hat \
  --hped exp_hla-typ_GEUV.hped \
  --out MyNomenCleaner/exp_hla-typ_GEUV_hg19.2field \
  --2field \
  --imgt 3320

• bmarkergenerator
  python3 HATK.py
  --bmarkergenerator
  --chped MyNomenCleaner/exp_hla-typ_GEUV_hg19.2field.chped
  --out MybMarkerGenerator/exp_hla-typ_GEUV.hg19
  --hg 19
  --dict-AA MyIMGT2Seq/HLA_DICTIONARY_AA.hg19.imgt3320
  --dict-SNPS MyIMGT2Seq/HLA_DICTIONARY_SNPS.hg19.imgt3320

[WansonChoi]

@mahoko

Hi, Thank you so much for your interest in HATK.

First, you have to add '--2field' argument in implementing IMGT2Seq. Otherwise, IMGT2Seq will generate 4-field nomenclature HLA sequence dictionary by default. I guess you are analyzing your SNPs in 2-field nomenclature considering you used '--2field' argument in NomenCleaner. Implementing bMarkerGenerator with 4-field HLA sequence dictionary and 2-field chped file will cause an implicit error.

Next, I found you didn't add '--variants' argument which takes the file path of your own SNP data in bMarkerGenrator.

=====================

bmarkergenerator
python3 HATK.py
--bmarkergenerator
--chped MyNomenCleaner/exp_hla-typ_GEUV_hg19.2field.chped
--out MybMarkerGenerator/exp_hla-typ_GEUV.hg19
--hg 19
--dict-AA MyIMGT2Seq/HLA_DICTIONARY_AA.hg19.imgt3320
--dict-SNPS MyIMGT2Seq/HLA_DICTIONARY_SNPS.hg19.imgt3320

=====================

If you don't, bMarkerGenerator will generate only HLA markers based on HLA alleles in chped file. In this case, the above FIELD MISMATCH could have caused the "No variant Error" because bMarkerGenerator couldn't have found any matched 2-field HLA alleles in the 4-field HLA dictionary.

So, (1) try IMGT2Seq again with '--2field' argument. (2) try bMarkerGenerator with the 2-field HLA dictionary.

In the (2), If you have your own SNP data, then don't forget to specify its file path to '--variants' argument.

Thanks,
Wanson.

[uedaMT]

Thank you very much for your reply. Your comments solved my problem!