bumblenick
commented
3 years ago I'm guessing you have non-human organisms
- Make sure you specify # autosomes ((if more than 22) numchrom:
- 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
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BiodeB
Dear Sir, I'm analyzing D-statistics for the first time using admixr in R and I'm getting below error,
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.
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