qpDstat not producing any D-statistics result
MrLocuace opened this issue · comments
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