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ERROR: insufficient number of blocks -- you need 5 blocks with non zero ABBA/BABA program terminating.

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Assessment

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

Research direction

Start with the d() call and the qpDstat output shown in the issue, focusing on the 2,142 SNPs and two reported jackknife blocks. Reproduce the command with the provided Eigenstrat prefix and determine whether the input or block configuration causes termination; done means documenting the cause and a supported resolution.

Written by the indexing model from the issue text.

Description

Dear Sir,
I'm analyzing D-statistics for the first time using admixr in R and I'm getting below error,

enough!
insufficient number of blocks -- you need 5 blocks with non zero ABBA/BABA program terminating

BEGINNING OF OUTPUT FILE
==================================================

qpDstat: parameter file: /tmp/RtmpkwhB54/qpDstat__1499352543.par
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
genotypename: /media/imdeb/Elements/2nd/Sequence/ABBATest/Admix/GB_eign/GB_snpS.geno
snpname: /media/imdeb/Elements/2nd/Sequence/ABBATest/Admix/GB_eign/GB_snpS.snp
indivname: /media/imdeb/Elements/2nd/Sequence/ABBATest/Admix/GB_eign/GB_snpS.ind
popfilename: /tmp/RtmpkwhB54/qpDstat__1499352543.pop
f4mode: YES
printsd: YES
## qpDstat version: 980
inbreed set NO
number of quadruples 1
  0           Blepharipa    1
  1           D_melanoga    1
  2           E_sorbilla    1
  3               B_mori    1
jackknife block size:     0.050
snps: 2142  indivs: 4
number of blocks for block jackknife: 2
nrows, ncols: 4 2142

==================================================
END OF OUTPUT FILE


Error: The output file we got from ADMIXTOOLS is truncated.
       Please examine the full output above and check for errors.

My objective is to investigate introgression in insect mt-DNA. Therefore I took 116 insect's mitochondrial protein coding genes, aligned and concatenated all the genes. Then I created a VCF file using snp-site tool, after that I converted it to EIGENSTRAT format by convertVCFtoEigenstrat.sh of Joana Meier. Now I'm implementing admixr but facing the above problem when I tried to estimate D-statistics.

prefix <- "/media/imdeb/Elements/2nd/Sequence/ABBATest/Admix/x/x11/x11_snpS"
snps <- eigenstrat(prefix)

pops <- c("Blepharipa","S_variegat","P_vanderpl","A_gambie","E_flavipal","D_mauritia")
result_D <- d(W = pops, X = "D_melanoga", Y = "E_sorbilla", Z = "B_mori", data = snps)

Kindly let me know how can I overcome this issue. As I understand either I need to increase number of blocks of decrease the size of of the blocks. So this is a humble request that please let me know how to do this.

Thank you,
Debajyoti

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