NEED HELP: not estimating the value of data provided #1
Description
Hi,
I was trying to see the founder event from my data, and while running the model, it doesn't fit. *.fit file is here to have a look:
param mean jk.mean jk.se
A None None None
t None None None
c None None None
NRMSD None None NA
The parameter I used are here:
genotypename: Test.eigenstratgeno
snpname: Test.snp
indivname: Test.ind
targetpop: NPG
outpop: RANDOM
outpopsize: 5
outputprefix: results/Test
binsize: 0.001
mindis: 0.001
maxdis: 0.3
maxpropsharingmissing: 1
minmaf: 0
haploid: NO
dopseudohaploid: NO
morgans: NO
onlyfit: NO
usefft: YES
qbins: 100
seed: 31
blocksizename: None
The log file say this:
Version 10.0
Test.eigenstratgeno
Test.snp
Test.ind
Output file name: results/Test
Target population: NPG
Outgroup population: defined by picking 5 random individuals, the new ind file is stored at: results/Test.ind
minMAF: 0.0
Assumes the genotypes are diploids
Using seed: 31
Distance bins: 0.1 cM to 30.0 cM by steps of 0.1 cM
Input distance in cM: True
Maximum proportion of allele sharing values that can be missing: 1.0
No block size file provided, will use the number of SNPs per chromosome as weights
Using FFT algorithm
qbins: 100
Calculation mode: auto
/!\ Given the nature of the data (==> diploid <==), setting calculation mode as: correlation
Random outgroup definition:
Number of outgroup individuals: 5
Analyzing NPG and using an outgroup population: OUTGROUP
There are 7 target and 5 outgroup samples
Chromosomes: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
Chrom: 1 -~- Range: [1; 1376233]
Raw nSNP: 1376233 MAF-filtered nSNP: 983805
Chrom: 2 -~- Range: [1376234; 2526222]
Raw nSNP: 1149989 MAF-filtered nSNP: 817731
Chrom: 3 -~- Range: [2526223; 3617439]
Raw nSNP: 1091217 MAF-filtered nSNP: 781537
Chrom: 4 -~- Range: [3617440; 4516182]
Raw nSNP: 898743 MAF-filtered nSNP: 637302
Chrom: 5 -~- Range: [4516183; 5350408]
Raw nSNP: 834226 MAF-filtered nSNP: 610649
Chrom: 6 -~- Range: [5350409; 6019720]
Raw nSNP: 669312 MAF-filtered nSNP: 474377
Chrom: 7 -~- Range: [6019721; 7037563]
Raw nSNP: 1017843 MAF-filtered nSNP: 771877
Chrom: 8 -~- Range: [7037564; 7653539]
Raw nSNP: 615976 MAF-filtered nSNP: 451048
Chrom: 9 -~- Range: [7653540; 8243970]
Raw nSNP: 590431 MAF-filtered nSNP: 424810
Chrom: 10 -~- Range: [8243971; 8917747]
Raw nSNP: 673777 MAF-filtered nSNP: 495074
Chrom: 11 -~- Range: [8917748; 9435416]
Raw nSNP: 517669 MAF-filtered nSNP: 366610
Chrom: 12 -~- Range: [9435417; 9902304]
Raw nSNP: 466888 MAF-filtered nSNP: 329830
Chrom: 13 -~- Range: [9902305; 10367026]
Raw nSNP: 464722 MAF-filtered nSNP: 331200
Chrom: 14 -~- Range: [10367027; 10895136]
Raw nSNP: 528110 MAF-filtered nSNP: 381728
Chrom: 15 -~- Range: [10895137; 11310443]
Raw nSNP: 415307 MAF-filtered nSNP: 279642
Chrom: 16 -~- Range: [11310444; 11721249]
Raw nSNP: 410806 MAF-filtered nSNP: 288674
Chrom: 17 -~- Range: [11721250; 12228272]
Raw nSNP: 507023 MAF-filtered nSNP: 367043
Chrom: 18 -~- Range: [12228273; 12638772]
Raw nSNP: 410500 MAF-filtered nSNP: 282945
Chrom: 19 -~- Range: [12638773; 13006442]
Raw nSNP: 367670 MAF-filtered nSNP: 258036
Chrom: 20 -~- Range: [13006443; 13506098]
Raw nSNP: 499656 MAF-filtered nSNP: 365520
Chrom: 21 -~- Range: [13506099; 13935538]
Raw nSNP: 429440 MAF-filtered nSNP: 311660
Chrom: 22 -~- Range: [13935539; 14294987]
Raw nSNP: 359449 MAF-filtered nSNP: 235557
Chrom: 23 -~- Range: [14294988; 15128218]
Raw nSNP: 833231 MAF-filtered nSNP: 570915
Chrom: 24 -~- Range: [15128219; 15494328]
Raw nSNP: 366110 MAF-filtered nSNP: 268529
Chrom: 25 -~- Range: [15494329; 15800598]
Raw nSNP: 306270 MAF-filtered nSNP: 222350
Chrom: 26 -~- Range: [15800599; 16017024]
Raw nSNP: 216426 MAF-filtered nSNP: 146381
Chrom: 27 -~- Range: [16017025; 16261675]
Raw nSNP: 244651 MAF-filtered nSNP: 190355
It took: 20.15 min
Substracting by cross-population allele sharing correlation
Running the exponential fitting with weighted jackknife
Chromosomes in input file:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
Chromosomes at the intersection of the two files:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
End
Kindly help in this regard