DReichLab / DReichLab/AdmixTools

qpDstat not producing any D-statistics result

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Description

Dear Nick,
I am trying to run qpDstat using the v44.3_HO_public database merged with my population of interest "Pop", with input files in EIGENSTRAT format (I also tried PACKEDANCESTRYMAP format). Some 20 minutes after running the following command:

qpDstat -p parfile_mbuti_x_pop1_pop2.txt [-l Mbuti.SDG] [-h Quechua.DG] > test1.log

the process gets killed and I get this log info (test1.log):

### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
genotypename: v44.3_HO_public_mergeit_pop.geno
snpname: v44.3_HO_public_mergeit_pop.snp
indivname: v44.3_HO_public_mergeit_pop.ind
poplistname: uniq_pops_list_v44.3_1240K_public.txt
popfilename: list_qpDstat1_mbuti_x_pop1_pop2.txt
f4mode: YES
printsd: YES
## qpDstat version: 970
packed geno read OK
end of inpack
number of quadruples 336
  0              Pop   11
  1         Ancestor.REF    1
  2             Href.REF    1
  3           Piapoco.DG    2
  4           Quechua.DG    2
  5              Mixe.DG    3
  6         Karitiana.DG    3
  7              Pima.DG    2

However, no D-statistics test ever gets computed.

Everything seems to be fine with the input files (here I only provide a few lines):

genotypename: v44.3_HO_public_mergeit_pop.geno:

222222222222202222212222221221222122221021222212111212221012210221...

snpname: v44.3_HO_public_mergeit_pop.snp:

      rs11807848     1        0.026711         1061166 T C
       rs4970421     1        0.028311         1108637 G A
       rs2887286     1        0.029335         1156131 T C
      rs79118541     1        0.029356         1157547 T C

indivname: v44.3_HO_public_mergeit_pop.ind:

         MAL-005 M Malawi_Yao
         MAL-009 M Malawi_Yao
         MAL-011 M Malawi_Chewa
         MAL-012 M Malawi_Chewa
         MAL-014 M Malawi_Chewa

poplistname: uniq_pops_list_v44.3_1240K_public.txt:

Mbuti.DG
Papuan.DG
Australian.DG
Ancestor.REF
Href.REF
Piapoco.DG
Quechua.DG

popfilename: list_qpDstat1_mbuti_x_pop1_pop2.txt:

Pop Ancestor.REF    Papuan.DG       Mbuti.DG
Pop Ancestor.REF    Australian.DG   Mbuti.DG
Pop Href.REF        Papuan.DG       Mbuti.DG
Pop Href.REF        Australian.DG   Mbuti.DG
Pop Piapoco.DG      Papuan.DG       Mbuti.DG
Pop Piapoco.DG      Australian.DG   Mbuti.DG
Pop Quechua.DG      Papuan.DG       Mbuti.DG

I really don't know why I am not getting any D-statistics results.
Please help !
Thanks a lot

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  3. Fork the repository and make your change on a branch.
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Research direction

Start by reproducing the qpDstat command with parfile_mbuti_x_pop1_pop2.txt and the listed EIGENSTRAT or PACKEDANCESTRYMAP inputs. Inspect the log after “number of quadruples 336” and the supplied genotype, SNP, individual, population-list, and population-file inputs; done means identifying why execution is killed before D-statistics are produced.

Written by the indexing model from the issue text.

Assessment

Tech stack
c
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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