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

Question

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

BiodeB opened this issue 3 years ago · comments

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

bumblenick · Answer 1 · Tue Aug 24 2021 06:02:39 GMT+0800 (China Standard Time)

I'm guessing you have non-human organisms 1. Make sure you specify # autosomes ((if more than 22) numchrom: 2. If you have "contigs" use blockname: -- described in the documentation to specify the snp blocks. With so few snps you can't expect tight standard errors., Nick

…

On Sat, Aug 21, 2021 at 11:16 PM Debajyoti Kabiraj ***@***.***> wrote: 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. 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#82>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77BZFJVILNSCVWODD4MDT6BT2HANCNFSM5CSPUYTQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

Debajyoti Kabiraj · Answer 2 · Wed Aug 25 2021 10:42:22 GMT+0800 (China Standard Time)

Dear Sir,

Thank you very much for your kind suggestions. I managed to run program after following the response of @Marvin02860 at [https://github.com//issues/54] .

Thanking you,
Debajyoti