Admixtools admixtools2 TUTORIAL for WINDOWS.

meyman · Dec 2, 2024

I'm new here. How can I open these files like this?

baeticvs · Dec 2, 2024

meyman said:
I'm new here. How can I open these files like this?

any text editor, pic related is Kate which is the default one for KDE

Jalisciense · Dec 3, 2024

Celtion said:
You can change the .fam or .ind file anytime before or after merging. Merging doesn't set the case/control selection into concrete so you don't need to remerge again if you change your mind.

When you convertf your Plink files to PAM it adds your family ID to the front of your individual ID with a colon; and then puts 'case' or 'control' in the 3rd column (instead of your family ID) depending on whether you had the 6th column in Plink format set to 2 or 1. So I recommend conforming to the PAM/Eigenstrat format and getting rid of case/control altogether and replacing it with your family ID (and deleting your family ID from the front of the individual ID).

So when converted to PAM/Eigenstrat your individual sample row might look like this:

Smith:John M Control

So I would change it to:

John M Smith

That way you won't have to worry about case/control at all since none of the samples in the AADR have case/control settings. Btw the 'M' is the sex column, not a middle name initial.

Thanks for everything bro, your help was essential for me to be able to do all this; you know a lot about qpAdm!!

I follow your advice and I could do the list subdataset with AADR v62.0_1240k, the issue is right pops that used to work in HO don't work anymore with the 1240k lol so I'll have to learn how to install and use the "rotation" stuff xdd

Celtion · Dec 5, 2024

Jalisciense said:
Thanks for everything bro, your help was essential for me to be able to do all this; you know a lot about qpAdm!!

I follow your advice and I could do the list subdataset with AADR v62.0_1240k, the issue is right pops that used to work in HO don't work anymore with the 1240k lol so I'll have to learn how to install and use the "rotation" stuff xdd

Well you're ahead of me in the practical use of qpAdm. As for myself I've actually only got as far as installing AdmixTools2 and loading the graphical interface, lol!

baeticvs · Dec 5, 2024

I'm getting horrible results when making PCAs with ancient samples, Im using the v62 1240k dataset

they all bunch up in the same place

here i changed the numoutevec number to 15 and added modern samples(red square) too

again the same problem, they all plot more or less together not making sense, except for the modern samples

Celtion · Dec 5, 2024

baeticvs said:
I'm getting horrible results when making PCAs with ancient samples, Im using the v62 1240k dataset
View attachment 17262
they all bunch up in the same place

here i changed the numoutevec number to 15 and added modern samples(red square) too
View attachment 17264
again the same problem, they all plot more or less together not making sense, except for the modern samples

Probably because most of the ancient samples have large amounts of missingness which has a wildcard effect, matching variants when it shouldn't thereby reducing accuracy. You will probably need to filter out some of the missingness and maybe prune for Linkage Disequilibrium. What format are your files in?

baeticvs · Dec 5, 2024

Celtion said:
Probably because most of the ancient samples have large amounts of missingness which has a wildcard effect, matching variants when it shouldn't thereby reducing accuracy. You will probably need to filter out some of the missingness and maybe prune for Linkage Disequilibrium. What format are your files in?

Im using eigenstrat format files and I tried not using low snp count samples

Celtion · Dec 5, 2024

baeticvs said:
Im using eigenstrat format files and I tried not using low snp count samples

Okay. Probably don't worry about the filtering and LD-pruning – I think it's more pertinent to admixture breakdowns than PCA. Just make sure you only use modern populations to set the vectors. Then you can project the ancient (and modern) plots on top of those.
This article here explains some of the problems encountered with ancient dna PCA plots:

Factor analysis of ancient population genomic samples - Nature Communications

Principal component analysis is often used in studies of ancient DNA, but does not account for the age of the samples. Here, the authors present a factor analysis (FA) which corrects for this by including the effect of allele frequency drift over time.

www.nature.com

Jalisciense · Dec 7, 2024

Celtion said:
Well you're ahead of me in the practical use of qpAdm. As for myself I've actually only got as far as installing AdmixTools2 and loading the graphical interface, lol!

We could be a team already bro, you explain how to install all these things and I run them

Celtion · Dec 8, 2024

baeticvs said:
I'm getting horrible results when making PCAs with ancient samples, Im using the v62 1240k dataset
View attachment 17262
they all bunch up in the same place

here i changed the numoutevec number to 15 and added modern samples(red square) too
View attachment 17264
again the same problem, they all plot more or less together not making sense, except for the modern samples

Btw have you tried using the HO set? I've noticed some studies are using the HO set for PCA as the ancient samples have been filtered on the Human Origins dataset. Also the lower snp count is less of an issue with PCA as the point of it is to reduce complex data to be visualised in 2 dimensions.

meyman · Dec 20, 2024

baeticvs said:
any text editor, pic related is Kate which is the default one for KDE

What is the name of the screen used in this screenshot?

Jovialis · Dec 20, 2024

I have attempted to replicate the outgroups from Lazaridis et al. 2018 pre-print, here in included qpwave. I didn't modify the FAM either, this is using the populations as they are in the vanilla IND/FAM:

Code:

library(admixtools)
library(tidyverse)

prefix <- "D:\\Bioinformatics\\01_Admixtools_Dataset\\v62.0_1240K_HO_Jovialis_Plink\\v62.0_1240K_HO_Jovialis"

# Define populations
target <- c('Jovialis')
left <- c('Greece_Crete_HgCharalambos_EMBA.AG', 'Italy_Ordona_Daunian.SG')
right <- c('Ethiopia_4500BP.AG', 'Russia_UstIshim_IUP.DG', 'China_Tianyuan.AG.BY.AA',
           'ONG.SG', 'Han.DG', 'Papuan.DG', 'Russia_Kostenki14_UP.AG.BY.AA',
           'Belgium_GoyetQ116_1_UP.AG', 'Russia_Sunghir_UP.SG', 'Italy_Epigravettian.AG.BY.AA',
           'Georgia_Dzudzuana_UP.AG', 'Russia_AfontovaGora3_UP.AG',
           'Czechia_Gravettian.AG.BY.AA', 'Russia_MA1_UP.SG')

# Step 1: Run qpWave to validate left and right populations
qpwave_results <- qpwave(data = prefix, left = left, right = right, verbose = TRUE)

# Print qpWave results
cat("qpWave Rank Drop Results:\n")
print(qpwave_results$rankdrop)

# Step 2: Evaluate qpWave results to determine if left populations are distinguishable
if (min(qpwave_results$rankdrop$p) > 0.01) {
  cat("\nqpWave passed validation. Proceeding with qpAdm...\n")
 
  # Step 3: Run qpAdm for target population
  results <- qpadm(prefix, left, right, target, allsnps = TRUE)
 
  # Print qpAdm results
  cat("\nqpAdm Admixture Weights:\n")
  print(results$weights)
 
  cat("\nqpAdm Population Drop Results:\n")
  print(results$popdrop)
 
} else {
  cat("\nqpWave failed validation. Refine left or right populations and retry.\n")
}

Jovialis · Dec 20, 2024

baeticvs said:
I'm getting horrible results when making PCAs with ancient samples, Im using the v62 1240k dataset
View attachment 17262
they all bunch up in the same place

here i changed the numoutevec number to 15 and added modern samples(red square) too
View attachment 17264
again the same problem, they all plot more or less together not making sense, except for the modern samples

Try to replicate this:

Projecting ancient samples

This Vignette provides an example of how to project ancient DNA onto modern data using the smartsnp package.

christianhuber.github.io

The ancient populations need to be projected against the Modern ones, because the ancient samples have a high level of missingness and poor quality. Thus they are optimally projected in a way deferring to the modern pops. In the end it is all relative, because you want to see how modern pops compare to them. Seems counter intuitive, but we are not modeling the modern pops based on aDNA in a sense.

Jalisciense · Dec 25, 2024

eupator said:
You can also use the following command to calculate FST distances to a target population.

Here, I am going to do just that by comparing various moderns to the Israel_Natufian_published samples:

fst(prefix, pop1 = "Israel_Natufian_published", pop2 = c("Egyptian", "Greek", "Lebanese", "Jordanian", "Saudi", "Somali"))

The results look like this (lower is closer, taking the standard error into account):

A tibble: 6 × 4
pop1 pop2 est se

1 Israel_Natufian_published Egyptian 0.0715 0.00702
2 Israel_Natufian_published Greek 0.0874 0.00729
3 Israel_Natufian_published Jordanian 0.0789 0.00720
4 Israel_Natufian_published Lebanese 0.0735 0.00728
5 Israel_Natufian_published Saudi 0.0760 0.00755
6 Israel_Natufian_published Somali 0.109 0.00701

It's good practice not to mix .DG/.SG samples with non .DG/.SG, because there is inherent bias towards the first, if you absolutely need to do this, you can adjust the command by adding: adjust_pseudohaploid = FALSE, at the end of the command.

"It's good practice not to mix .DG/.SG samples with non .DG/.SG, because there is inherent bias towards the first, if you absolutely need to do this, you can adjust the command by adding: adjust_pseudohaploid = FALSE, at the end of the command."

If in AdmixTools2 is adjust_pseudohaploid = FALSE, then in AdmixTools1 is Inbreed: NO? Or am I wrong?

meyman · Dec 29, 2024

prefix = "C:/Users/spart/Downloads/meyman/data/v54.1.p1_1240K_public/v54.1.p1_1240K_public"
my_f2_dir = "C:/Users/spart/Downloads/meyman/mdir"
library(admixtools)
library(tidyverse)

Error in anygeno_to_aftable(pref, inds = inds, pops = pops, format = format, :
Genotype files not found!
can me help any one i cant solve..I tried everything written

Jalisciense · Dec 29, 2024

meyman said:
prefix = "C:/Users/spart/Downloads/meyman/data/v54.1.p1_1240K_public/v54.1.p1_1240K_public"
my_f2_dir = "C:/Users/spart/Downloads/meyman/mdir"
library(admixtools)
library(tidyverse)

Error in anygeno_to_aftable(pref, inds = inds, pops = pops, format = format, :
Genotype files not found!
can me help any one i cant solve..I tried everything written

I haven't installed AdmixTools2 and I'm not an expert, but I see you have double "v54.1.p1_1240K_public" in your directory route.

Try this:

Code:

prefix = "C:/Users/spart/Downloads/meyman/data/v54.1.p1_1240K_public"

my_f2_dir = "C:/Users/spart/Downloads/meyman/mdir"

library(admixtools)

library(tidyverse)

meyman · Dec 29, 2024

Jalisciense said:
I haven't installed AdmixTools2 and I'm not an expert, but I see you have double "v54.1.p1_1240K_public" in your directory route.

Try this:

Code:

prefix = "C:/Users/spart/Downloads/meyman/data/v54.1.p1_1240K_public" my_f2_dir = "C:/Users/spart/Downloads/meyman/mdir" library(admixtools) library(tidyverse)

I tried that too.. I tried everything that was written.

meyman · Dec 29, 2024

prefix = "C:/Users/spart/Downloads/meyman/data/v54.1.p1_1240K_public"
my_f2_dir = "C:/Users/spart/Downloads/meyman/mdir"
library(admixtools)
library(tidyverse)

> target = c('Greece_Roman')
> left= c('Turkey_Barcin_LN.SG','Georgia_Kotias.SG','Armenian.DG')
> right = c('Mbuti.DG', 'Ethiopia_4500BP', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Peru_EIP_Moche', 'Ignore_Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Russia_Samara_EBA_Yamnaya', 'Ukraine_VertebaCave_CordedWare', 'Armenia_LBA.SG', 'ONG.SG')
> mypops = c('Mbuti.DG', 'Ethiopia_4500BP', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Peru_EIP_Moche', 'Ignore_Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Russia_Samara_EBA_Yamnaya', 'Ukraine_VertebaCave_CordedWare', 'Armenia_LBA.SG', 'ONG.SG')
> extract_f2(prefix, my_f2_dir, pops = mypops, overwrite = TRUE, maxmiss = 1)

Error in anygeno_to_aftable(pref, inds = inds, pops = pops, format = format, :
Genotype files not found!

what i have to do

Stefano · Feb 10, 2025

Hi, since i was interested in modeling myself with qpAdm i decided to try Insight on Ancestry, a site that offers qpAdm service for 33 dollars.
I sent my raw data and received the results.

What do you think, are they legit? Here is how they compare to official and simulated G25.
Target: StefanoMerged_scaled
Distance: 0.0284% / 0.02840093
62.1 Anatolia_Barcin_N
33.8 Yamnaya
3.6 WHG
0.5 Yellow_river_LN

Target: simulated_g25_scaled
Distance: 0.0243% / 0.02427442
61.6 Anatolia_Barcin_N
33.4 Yamnaya
5.0 WHG

Target:StefanoMerged_scaled
Distance: 0.0143% / 0.01426600
59.9 CisalpineGauls_Verona_LIA
39.2 Italy_Imperial.SG
0.9 Hungary_Langobard

Target: simulated_g25_scaled
Distance: 0.0097% / 0.00968399
66.9 CisalpineGauls_Verona_LIA
31.8 Italy_Imperial.SG
1.3 Hungary_Langobard

Here is the full qpAdm output, can please someone expert check it? Was it done right?

Code:

qpAdm: parameter file: parqpAdmix.txt
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
indivname: Work.ind
snpname: Work.snp
genotypename: Work.geno
basepop: Han.DG
popleft: left.txt
popright: right.txt
inbreed: NO
allsnps: YES
details: YES
##  qpAdm -p parqpAdmix.txt
## qpAdm version: 2050
seed: 2018941576
basepop set: Han.DG
inbreed set NO
tmp: /tmp/fsx.2760

left pops:
             Stefano      1
Russia_Samara_EBA_Yamnaya     10
                 WHG      4
            Turkey_N     25

right pops:
            Mbuti.DG     10
                 EHG      5
                 CHG      2
                ESHG     10
   Turkey_Boncuklu_N      5
          Levant_PPN     14
     Israel_Natufian      5
    Iran_GanjDareh_N      8
Russia_AfontovaGora3      1
Serbia_IronGates_Mesolithic     32

codimension 1
f4info:
f4rank: 2 dof:      7 chisq:    12.550 tail:         0.0838528733 dofdiff:      9 chisqdiff:   -12.550 taildiff:                    1
B:
          scale     1.000     1.000
            EHG     1.105     0.762
            CHG    -0.110     0.839
           ESHG     0.418     0.350
Turkey_Boncuklu_N    -0.868    -0.921
     Levant_PPN    -0.881    -0.714
Israel_Natufian    -0.673    -0.650
Iran_GanjDareh_N    -0.228     0.714
Russia_AfontovaGora3     0.730     1.559
Serbia_IronGates_Mesolithic     2.242    -1.694
A:
          scale    76.363   137.531
Russia_Samara_EBA_Yamnaya     0.687     1.349
            WHG     1.514    -0.883
       Turkey_N    -0.485    -0.633


full rank
f4info:
f4rank: 3 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      7 chisqdiff:    12.550 taildiff:         0.0838528733
B:
          scale    71.070    46.561   136.315
            EHG     1.369     0.882    -1.172
            CHG     0.391    -0.429    -0.639
           ESHG     0.473     0.261    -0.656
Turkey_Boncuklu_N    -1.134    -0.482     1.454
     Levant_PPN    -0.995    -0.554     1.331
Israel_Natufian    -0.800    -0.366     1.158
Iran_GanjDareh_N     0.337    -0.428    -0.270
Russia_AfontovaGora3     1.902     0.442    -0.959
Serbia_IronGates_Mesolithic     0.320     2.630    -0.755
A:
          scale     1.732     1.732     1.732
Russia_Samara_EBA_Yamnaya     1.732     0.000     0.000
            WHG     0.000     1.732     0.000
       Turkey_N     0.000     0.000     1.732


best coefficients:     0.326     0.052     0.623
totmean:      0.326     0.052     0.623
zzevarboot
    0.356568388     0.055796891     0.587634721
    0.008231526     0.009704518
    0.019815143    -0.006129171
   -0.006876254    -0.005306588
zzevarboot2
    0.294458384     0.046877694     0.658663922
    0.009826773    -0.009841731
    0.019827094     0.006830521
   -0.005804211     0.003913651
boot mean:     0.326     0.051     0.623
bootstrap saimpling of F-coeffs: 1000
zzjmean     0.326     0.051     0.623
      std. errors:     0.027     0.015     0.021

error covariance (* 1,000,000)
       704       -246       -458
      -246        227         19
      -458         19        439


summ: Stefano    3      0.083853     0.326     0.051     0.623        704       -246       -458        227         19   ...
       439

    fixed pat  wt  dof     chisq       tail prob
          000  0     7    12.550       0.0838529     0.326     0.052     0.623
          001  1     8   733.463               0     1.026    -0.026     0.000  infeasible
          010  1     8    24.325      0.00202108     0.384     0.000     0.616
          100  1     8   163.033               0     0.000     0.167     0.833
          011  2     9   735.896               0     1.000     0.000     0.000
          101  2     9  2871.169               0     0.000     1.000     0.000
          110  2     9   344.975               0     0.000     0.000     1.000
best pat:          000        0.0838529              -  -
best pat:          010       0.00202108  chi(nested):    11.775 p-value for nested model:     0.000600409
best pat:          110      7.27034e-69  chi(nested):   320.650 p-value for nested model:     1.04566e-71

coeffs:     0.326     0.052     0.623

## dscore:: f_4(Base, Fit, Rbase, right2)
## genstat:: f_4(Base, Fit, right1, right2)

details: Russia_Samara_EBA_Yamnaya                  EHG     0.019262   12.674809
details:                  WHG                  EHG     0.018943   10.994216
details:             Turkey_N                  EHG    -0.008594   -5.737769
dscore:                  EHG f4:     0.001901 Z:     1.320143

details: Russia_Samara_EBA_Yamnaya                  CHG     0.005504    3.301351
details:                  WHG                  CHG    -0.009220   -5.037312
details:             Turkey_N                  CHG    -0.004687   -2.979976
dscore:                  CHG f4:    -0.001600 Z:    -1.031556

details: Russia_Samara_EBA_Yamnaya                 ESHG     0.006653    5.521117
details:                  WHG                 ESHG     0.005611    4.223465
details:             Turkey_N                 ESHG    -0.004815   -4.241948
dscore:                 ESHG f4:    -0.000541 Z:    -0.488491

details: Russia_Samara_EBA_Yamnaya    Turkey_Boncuklu_N    -0.015953  -10.920864
details:                  WHG    Turkey_Boncuklu_N    -0.010342   -6.587571
details:             Turkey_N    Turkey_Boncuklu_N     0.010664    7.728693
dscore:    Turkey_Boncuklu_N f4:     0.000909 Z:     0.674108

details: Russia_Samara_EBA_Yamnaya           Levant_PPN    -0.013995   -9.355710
details:                  WHG           Levant_PPN    -0.011888   -7.758160
details:             Turkey_N           Levant_PPN     0.009763    7.093255
dscore:           Levant_PPN f4:     0.000906 Z:     0.667221

details: Russia_Samara_EBA_Yamnaya      Israel_Natufian    -0.011254   -5.488518
details:                  WHG      Israel_Natufian    -0.007851   -3.648711
details:             Turkey_N      Israel_Natufian     0.008494    4.403457
dscore:      Israel_Natufian f4:     0.001217 Z:     0.638692

details: Russia_Samara_EBA_Yamnaya     Iran_GanjDareh_N     0.004749    3.745552
details:                  WHG     Iran_GanjDareh_N    -0.009194   -6.507243
details:             Turkey_N     Iran_GanjDareh_N    -0.001984   -1.632945
dscore:     Iran_GanjDareh_N f4:    -0.000161 Z:    -0.136284

details: Russia_Samara_EBA_Yamnaya Russia_AfontovaGora3     0.026766   11.265759
details:                  WHG Russia_AfontovaGora3     0.009496    3.682707
details:             Turkey_N Russia_AfontovaGora3    -0.007037   -3.138894
dscore: Russia_AfontovaGora3 f4:     0.004829 Z:     2.178102

details: Russia_Samara_EBA_Yamnaya Serbia_IronGates_Mesolithic     0.004507    3.087822
details:                  WHG Serbia_IronGates_Mesolithic     0.056493   35.432490
details:             Turkey_N Serbia_IronGates_Mesolithic    -0.005539   -3.984981
dscore: Serbia_IronGates_Mesolithic f4:     0.000929 Z:     0.683563

gendstat:             Mbuti.DG                  EHG     1.320
gendstat:             Mbuti.DG                  CHG    -1.032
gendstat:             Mbuti.DG                 ESHG    -0.488
gendstat:             Mbuti.DG    Turkey_Boncuklu_N     0.674
gendstat:             Mbuti.DG           Levant_PPN     0.667
gendstat:             Mbuti.DG      Israel_Natufian     0.639
gendstat:             Mbuti.DG     Iran_GanjDareh_N    -0.136
gendstat:             Mbuti.DG Russia_AfontovaGora3     2.178
gendstat:             Mbuti.DG Serbia_IronGates_Mesolithic     0.684
gendstat:                  EHG                  CHG    -2.361
gendstat:                  EHG                 ESHG    -1.925
gendstat:                  EHG    Turkey_Boncuklu_N    -0.736
gendstat:                  EHG           Levant_PPN    -0.663
gendstat:                  EHG      Israel_Natufian    -0.324
gendstat:                  EHG     Iran_GanjDareh_N    -1.550
gendstat:                  EHG Russia_AfontovaGora3     1.476
gendstat:                  EHG Serbia_IronGates_Mesolithic    -0.885
gendstat:                  CHG                 ESHG     0.717
gendstat:                  CHG    Turkey_Boncuklu_N     1.747
gendstat:                  CHG           Levant_PPN     1.551
gendstat:                  CHG      Israel_Natufian     1.313
gendstat:                  CHG     Iran_GanjDareh_N     1.088
gendstat:                  CHG Russia_AfontovaGora3     2.848
gendstat:                  CHG Serbia_IronGates_Mesolithic     1.735
gendstat:                 ESHG    Turkey_Boncuklu_N     1.111
gendstat:                 ESHG           Levant_PPN     1.132
gendstat:                 ESHG      Israel_Natufian     0.905
gendstat:                 ESHG     Iran_GanjDareh_N     0.336
gendstat:                 ESHG Russia_AfontovaGora3     2.593
gendstat:                 ESHG Serbia_IronGates_Mesolithic     1.209
gendstat:    Turkey_Boncuklu_N           Levant_PPN    -0.002
gendstat:    Turkey_Boncuklu_N      Israel_Natufian     0.161
gendstat:    Turkey_Boncuklu_N     Iran_GanjDareh_N    -0.883
gendstat:    Turkey_Boncuklu_N Russia_AfontovaGora3     1.819
gendstat:    Turkey_Boncuklu_N Serbia_IronGates_Mesolithic     0.018
gendstat:           Levant_PPN      Israel_Natufian     0.166
gendstat:           Levant_PPN     Iran_GanjDareh_N    -0.822
gendstat:           Levant_PPN Russia_AfontovaGora3     1.742
gendstat:           Levant_PPN Serbia_IronGates_Mesolithic     0.018
gendstat:      Israel_Natufian     Iran_GanjDareh_N    -0.696
gendstat:      Israel_Natufian Russia_AfontovaGora3     1.360
gendstat:      Israel_Natufian Serbia_IronGates_Mesolithic    -0.148
gendstat:     Iran_GanjDareh_N Russia_AfontovaGora3     2.404
gendstat:     Iran_GanjDareh_N Serbia_IronGates_Mesolithic     0.896
gendstat: Russia_AfontovaGora3 Serbia_IronGates_Mesolithic    -1.888

worst Z-score with right hand mix
f4(Target, Fit, Base, mix of Right pops;  Z:    -3.543 sum:     1.000
                           EHG   -54.579
                           CHG    61.133
                          ESHG    65.493
             Turkey_Boncuklu_N   -19.356
                    Levant_PPN   -22.325
               Israel_Natufian   -10.167
              Iran_GanjDareh_N    15.413
          Russia_AfontovaGora3   -43.705
   Serbia_IronGates_Mesolithic     9.092

removing /tmp/fsx.2760
oldmode set: terminating
##end of qpAdm:        1.348 seconds cpu        0.000 Mbytes in use

Code:

qpAdm: parameter file: parqpAdmix.txt
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
indivname: Work.ind
snpname: Work.snp
genotypename: Work.geno
basepop: Han.DG
popleft: left.txt
popright: right.txt
inbreed: NO
allsnps: YES
details: YES
##  qpAdm -p parqpAdmix.txt
## qpAdm version: 2050
seed: 2007363432
basepop set: Han.DG
inbreed set NO
tmp: /tmp/fsx.4450

left pops:
             Stefano      1
    Italy_Verona_LIA     16
   Italy_Imperial.SG     35
   Hungary_Langobard     12

right pops:
            Mbuti.DG     10
                 EHG      5
                 CHG      2
                 WHG      4
            Turkey_N     25
                ESHG     10
          Levant_PPN     14
     Israel_Natufian      5
    Iran_GanjDareh_N      8
Russia_AfontovaGora3      1
Serbia_IronGates_Mesolithic     32

codimension 1
f4info:
f4rank: 2 dof:      8 chisq:    15.089 tail:         0.0574365379 dofdiff:     10 chisqdiff:   -15.089 taildiff:                    1
B:
          scale     1.000     1.000
            EHG     1.443     1.031
            CHG    -0.010     0.873
            WHG     1.710    -1.451
       Turkey_N     0.213    -0.838
           ESHG     0.488    -0.187
     Levant_PPN     0.054     0.539
Israel_Natufian     0.122    -0.092
Iran_GanjDareh_N    -0.021     1.997
Russia_AfontovaGora3     1.313     0.882
Serbia_IronGates_Mesolithic     1.722    -0.516
A:
          scale   191.945   976.539
Italy_Verona_LIA     0.643    -0.616
Italy_Imperial.SG    -0.862     0.370
Hungary_Langobard     1.358     1.576


full rank
f4info:
f4rank: 3 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      8 chisqdiff:    15.089 taildiff:         0.0574365379
B:
          scale   330.192   160.886   164.181
            EHG     0.478    -1.428     1.529
            CHG    -1.049    -0.369    -0.187
            WHG     1.618    -1.627     1.305
       Turkey_N    -0.754    -0.772    -0.525
           ESHG     0.126    -0.585     0.327
     Levant_PPN    -0.981    -0.463    -0.255
Israel_Natufian    -0.549    -0.436    -0.196
Iran_GanjDareh_N    -1.144    -0.218     0.159
Russia_AfontovaGora3     1.313    -0.864     1.849
Serbia_IronGates_Mesolithic     1.083    -1.743     1.413
A:
          scale     1.732     1.732     1.732
Italy_Verona_LIA     1.732     0.000     0.000
Italy_Imperial.SG     0.000     1.732     0.000
Hungary_Langobard     0.000     0.000     1.732


best coefficients:     0.465     0.462     0.073
totmean:      0.465     0.462     0.073
zzevarboot
    0.613122710     0.371310596     0.015566694
    0.002705131    -0.000639406
   -0.004746560     0.000999248
    0.006672632     0.001349206
zzevarboot2
    0.329188571     0.541284222     0.129527207
    0.003852340    -0.000838923
   -0.004154070     0.000160643
    0.007568962     0.001460778
boot mean:     0.467     0.462     0.071
bootstrap saimpling of F-coeffs: 1000
zzjmean     0.467     0.462     0.071
      std. errors:     0.157     0.070     0.117

error covariance (* 1,000,000)
     24771      -8041     -16730
     -8041       4933       3108
    -16730       3108      13622


summ: Stefano    3      0.057437     0.467     0.462     0.071      24771      -8041     -16730       4933       3108   ...
     13622

    fixed pat  wt  dof     chisq       tail prob
          000  0     8    15.089       0.0574365     0.465     0.462     0.073
          001  1     9    15.756       0.0721479     0.556     0.444     0.000
          010  1     9    55.867     8.32361e-09     1.306     0.000    -0.306  infeasible
          100  1     9    23.955      0.00437272     0.000     0.611     0.389
          011  2    10    63.056     9.52791e-10     1.000     0.000     0.000
          101  2    10    88.324     1.15035e-14     0.000     1.000     0.000
          110  2    10   177.595               0     0.000     0.000     1.000
best pat:          000        0.0574365              -  -
best pat:          100       0.00437272  chi(nested):     8.866 p-value for nested model:      0.00290512
best pat:          011      9.52791e-10 not nested

coeffs:     0.465     0.462     0.073

## dscore:: f_4(Base, Fit, Rbase, right2)
## genstat:: f_4(Base, Fit, right1, right2)

details:     Italy_Verona_LIA                  EHG     0.001448    1.003195
details:    Italy_Imperial.SG                  EHG    -0.008878   -6.215792
details:    Hungary_Langobard                  EHG     0.009311    6.395817
dscore:                  EHG f4:    -0.002750 Z:    -1.950686

details:     Italy_Verona_LIA                  CHG    -0.003176   -2.132666
details:    Italy_Imperial.SG                  CHG    -0.002296   -1.524077
details:    Hungary_Langobard                  CHG    -0.001137   -0.729641
dscore:                  CHG f4:    -0.002621 Z:    -1.775883

details:     Italy_Verona_LIA                  WHG     0.004900    3.299876
details:    Italy_Imperial.SG                  WHG    -0.010114   -6.848169
details:    Hungary_Langobard                  WHG     0.007947    5.289474
dscore:                  WHG f4:    -0.001817 Z:    -1.247297

details:     Italy_Verona_LIA             Turkey_N    -0.002283   -2.065800
details:    Italy_Imperial.SG             Turkey_N    -0.004801   -4.304503
details:    Hungary_Langobard             Turkey_N    -0.003198   -2.782188
dscore:             Turkey_N f4:    -0.003514 Z:    -3.215169

details:     Italy_Verona_LIA                 ESHG     0.000383    0.340282
details:    Italy_Imperial.SG                 ESHG    -0.003636   -3.233681
details:    Hungary_Langobard                 ESHG     0.001993    1.774249
dscore:                 ESHG f4:    -0.001357 Z:    -1.232747

details:     Italy_Verona_LIA           Levant_PPN    -0.002971   -2.153003
details:    Italy_Imperial.SG           Levant_PPN    -0.002879   -2.095065
details:    Hungary_Langobard           Levant_PPN    -0.001554   -1.114981
dscore:           Levant_PPN f4:    -0.002825 Z:    -2.085862

details:     Italy_Verona_LIA      Israel_Natufian    -0.001664   -0.838775
details:    Italy_Imperial.SG      Israel_Natufian    -0.002712   -1.390892
details:    Hungary_Langobard      Israel_Natufian    -0.001193   -0.604499
dscore:      Israel_Natufian f4:    -0.002114 Z:    -1.095678

details:     Italy_Verona_LIA     Iran_GanjDareh_N    -0.003465   -2.939604
details:    Italy_Imperial.SG     Iran_GanjDareh_N    -0.001357   -1.167068
details:    Hungary_Langobard     Iran_GanjDareh_N     0.000968    0.800455
dscore:     Iran_GanjDareh_N f4:    -0.002167 Z:    -1.881145

details:     Italy_Verona_LIA Russia_AfontovaGora3     0.003976    1.792318
details:    Italy_Imperial.SG Russia_AfontovaGora3    -0.005369   -2.406227
details:    Hungary_Langobard Russia_AfontovaGora3     0.011259    4.887681
dscore: Russia_AfontovaGora3 f4:     0.000189 Z:     0.086182

details:     Italy_Verona_LIA Serbia_IronGates_Mesolithic     0.003279    2.428296
details:    Italy_Imperial.SG Serbia_IronGates_Mesolithic    -0.010834   -8.029272
details:    Hungary_Langobard Serbia_IronGates_Mesolithic     0.008608    6.257959
dscore: Serbia_IronGates_Mesolithic f4:    -0.002855 Z:    -2.150311

gendstat:             Mbuti.DG                  EHG    -1.951
gendstat:             Mbuti.DG                  CHG    -1.776
gendstat:             Mbuti.DG                  WHG    -1.247
gendstat:             Mbuti.DG             Turkey_N    -3.215
gendstat:             Mbuti.DG                 ESHG    -1.233
gendstat:             Mbuti.DG           Levant_PPN    -2.086
gendstat:             Mbuti.DG      Israel_Natufian    -1.096
gendstat:             Mbuti.DG     Iran_GanjDareh_N    -1.881
gendstat:             Mbuti.DG Russia_AfontovaGora3     0.086
gendstat:             Mbuti.DG Serbia_IronGates_Mesolithic    -2.150
gendstat:                  EHG                  CHG     0.087
gendstat:                  EHG                  WHG     0.718
gendstat:                  EHG             Turkey_N    -0.644
gendstat:                  EHG                 ESHG     1.126
gendstat:                  EHG           Levant_PPN    -0.050
gendstat:                  EHG      Israel_Natufian     0.306
gendstat:                  EHG     Iran_GanjDareh_N     0.434
gendstat:                  EHG Russia_AfontovaGora3     1.477
gendstat:                  EHG Serbia_IronGates_Mesolithic    -0.095
gendstat:                  CHG                  WHG     0.505
gendstat:                  CHG             Turkey_N    -0.685
gendstat:                  CHG                 ESHG     0.894
gendstat:                  CHG           Levant_PPN    -0.129
gendstat:                  CHG      Israel_Natufian     0.239
gendstat:                  CHG     Iran_GanjDareh_N     0.345
gendstat:                  CHG Russia_AfontovaGora3     1.253
gendstat:                  CHG Serbia_IronGates_Mesolithic    -0.162
gendstat:                  WHG             Turkey_N    -1.525
gendstat:                  WHG                 ESHG     0.353
gendstat:                  WHG           Levant_PPN    -0.718
gendstat:                  WHG      Israel_Natufian    -0.148
gendstat:                  WHG     Iran_GanjDareh_N    -0.254
gendstat:                  WHG Russia_AfontovaGora3     0.919
gendstat:                  WHG Serbia_IronGates_Mesolithic    -1.385
gendstat:             Turkey_N                 ESHG     2.089
gendstat:             Turkey_N           Levant_PPN     0.694
gendstat:             Turkey_N      Israel_Natufian     0.791
gendstat:             Turkey_N     Iran_GanjDareh_N     1.333
gendstat:             Turkey_N Russia_AfontovaGora3     1.784
gendstat:             Turkey_N Serbia_IronGates_Mesolithic     0.704
gendstat:                 ESHG           Levant_PPN    -1.153
gendstat:                 ESHG      Israel_Natufian    -0.388
gendstat:                 ESHG     Iran_GanjDareh_N    -0.731
gendstat:                 ESHG Russia_AfontovaGora3     0.751
gendstat:                 ESHG Serbia_IronGates_Mesolithic    -1.270
gendstat:           Levant_PPN      Israel_Natufian     0.376
gendstat:           Levant_PPN     Iran_GanjDareh_N     0.499
gendstat:           Levant_PPN Russia_AfontovaGora3     1.345
gendstat:           Levant_PPN Serbia_IronGates_Mesolithic    -0.024
gendstat:      Israel_Natufian     Iran_GanjDareh_N    -0.026
gendstat:      Israel_Natufian Russia_AfontovaGora3     0.874
gendstat:      Israel_Natufian Serbia_IronGates_Mesolithic    -0.380
gendstat:     Iran_GanjDareh_N Russia_AfontovaGora3     1.140
gendstat:     Iran_GanjDareh_N Serbia_IronGates_Mesolithic    -0.559
gendstat: Russia_AfontovaGora3 Serbia_IronGates_Mesolithic    -1.472

worst Z-score with right hand mix
f4(Target, Fit, Base, mix of Right pops;  Z:    -3.852 sum:     1.000
                           EHG     0.254
                           CHG     0.060
                           WHG    -0.692
                      Turkey_N     1.268
                          ESHG    -0.218
                    Levant_PPN    -0.009
               Israel_Natufian    -0.026
              Iran_GanjDareh_N     0.101
          Russia_AfontovaGora3    -0.268
   Serbia_IronGates_Mesolithic     0.531

removing /tmp/fsx.4450
oldmode set: terminating
##end of qpAdm:        1.673 seconds cpu        0.000 Mbytes in use

qh777 · Feb 10, 2025

Stefano said:

Hi, since i was interested in modeling myself with qpAdm i decided to try Insight on Ancestry, a site that offers qpAdm service for 33 dollars.
I sent my raw data and received the results.
View attachment 17703 View attachment 17704
What do you think, are they legit? Here is how they compare to official and simulated G25.
Target: StefanoMerged_scaled
Distance: 0.0284% / 0.02840093
62.1 Anatolia_Barcin_N
33.8 Yamnaya
3.6 WHG
0.5 Yellow_river_LN

Target: simulated_g25_scaled
Distance: 0.0243% / 0.02427442
61.6 Anatolia_Barcin_N
33.4 Yamnaya
5.0 WHG

Target:StefanoMerged_scaled
Distance: 0.0143% / 0.01426600
59.9 CisalpineGauls_Verona_LIA
39.2 Italy_Imperial.SG
0.9 Hungary_Langobard

Target: simulated_g25_scaled
Distance: 0.0097% / 0.00968399
66.9 CisalpineGauls_Verona_LIA
31.8 Italy_Imperial.SG
1.3 Hungary_Langobard

Here is the full qpAdm output, can please someone expert check it? Was it done right?

Code:

qpAdm: parameter file: parqpAdmix.txt
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
indivname: Work.ind
snpname: Work.snp
genotypename: Work.geno
basepop: Han.DG
popleft: left.txt
popright: right.txt
inbreed: NO
allsnps: YES
details: YES
##  qpAdm -p parqpAdmix.txt
## qpAdm version: 2050
seed: 2018941576
basepop set: Han.DG
inbreed set NO
tmp: /tmp/fsx.2760

left pops:
             Stefano      1
Russia_Samara_EBA_Yamnaya     10
                 WHG      4
            Turkey_N     25

right pops:
            Mbuti.DG     10
                 EHG      5
                 CHG      2
                ESHG     10
   Turkey_Boncuklu_N      5
          Levant_PPN     14
     Israel_Natufian      5
    Iran_GanjDareh_N      8
Russia_AfontovaGora3      1
Serbia_IronGates_Mesolithic     32

codimension 1
f4info:
f4rank: 2 dof:      7 chisq:    12.550 tail:         0.0838528733 dofdiff:      9 chisqdiff:   -12.550 taildiff:                    1
B:
          scale     1.000     1.000
            EHG     1.105     0.762
            CHG    -0.110     0.839
           ESHG     0.418     0.350
Turkey_Boncuklu_N    -0.868    -0.921
     Levant_PPN    -0.881    -0.714
Israel_Natufian    -0.673    -0.650
Iran_GanjDareh_N    -0.228     0.714
Russia_AfontovaGora3     0.730     1.559
Serbia_IronGates_Mesolithic     2.242    -1.694
A:
          scale    76.363   137.531
Russia_Samara_EBA_Yamnaya     0.687     1.349
            WHG     1.514    -0.883
       Turkey_N    -0.485    -0.633


full rank
f4info:
f4rank: 3 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      7 chisqdiff:    12.550 taildiff:         0.0838528733
B:
          scale    71.070    46.561   136.315
            EHG     1.369     0.882    -1.172
            CHG     0.391    -0.429    -0.639
           ESHG     0.473     0.261    -0.656
Turkey_Boncuklu_N    -1.134    -0.482     1.454
     Levant_PPN    -0.995    -0.554     1.331
Israel_Natufian    -0.800    -0.366     1.158
Iran_GanjDareh_N     0.337    -0.428    -0.270
Russia_AfontovaGora3     1.902     0.442    -0.959
Serbia_IronGates_Mesolithic     0.320     2.630    -0.755
A:
          scale     1.732     1.732     1.732
Russia_Samara_EBA_Yamnaya     1.732     0.000     0.000
            WHG     0.000     1.732     0.000
       Turkey_N     0.000     0.000     1.732


best coefficients:     0.326     0.052     0.623
totmean:      0.326     0.052     0.623
zzevarboot
    0.356568388     0.055796891     0.587634721
    0.008231526     0.009704518
    0.019815143    -0.006129171
   -0.006876254    -0.005306588
zzevarboot2
    0.294458384     0.046877694     0.658663922
    0.009826773    -0.009841731
    0.019827094     0.006830521
   -0.005804211     0.003913651
boot mean:     0.326     0.051     0.623
bootstrap saimpling of F-coeffs: 1000
zzjmean     0.326     0.051     0.623
      std. errors:     0.027     0.015     0.021

error covariance (* 1,000,000)
       704       -246       -458
      -246        227         19
      -458         19        439


summ: Stefano    3      0.083853     0.326     0.051     0.623        704       -246       -458        227         19   ...
       439

    fixed pat  wt  dof     chisq       tail prob
          000  0     7    12.550       0.0838529     0.326     0.052     0.623
          001  1     8   733.463               0     1.026    -0.026     0.000  infeasible
          010  1     8    24.325      0.00202108     0.384     0.000     0.616
          100  1     8   163.033               0     0.000     0.167     0.833
          011  2     9   735.896               0     1.000     0.000     0.000
          101  2     9  2871.169               0     0.000     1.000     0.000
          110  2     9   344.975               0     0.000     0.000     1.000
best pat:          000        0.0838529              -  -
best pat:          010       0.00202108  chi(nested):    11.775 p-value for nested model:     0.000600409
best pat:          110      7.27034e-69  chi(nested):   320.650 p-value for nested model:     1.04566e-71

coeffs:     0.326     0.052     0.623

## dscore:: f_4(Base, Fit, Rbase, right2)
## genstat:: f_4(Base, Fit, right1, right2)

details: Russia_Samara_EBA_Yamnaya                  EHG     0.019262   12.674809
details:                  WHG                  EHG     0.018943   10.994216
details:             Turkey_N                  EHG    -0.008594   -5.737769
dscore:                  EHG f4:     0.001901 Z:     1.320143

details: Russia_Samara_EBA_Yamnaya                  CHG     0.005504    3.301351
details:                  WHG                  CHG    -0.009220   -5.037312
details:             Turkey_N                  CHG    -0.004687   -2.979976
dscore:                  CHG f4:    -0.001600 Z:    -1.031556

details: Russia_Samara_EBA_Yamnaya                 ESHG     0.006653    5.521117
details:                  WHG                 ESHG     0.005611    4.223465
details:             Turkey_N                 ESHG    -0.004815   -4.241948
dscore:                 ESHG f4:    -0.000541 Z:    -0.488491

details: Russia_Samara_EBA_Yamnaya    Turkey_Boncuklu_N    -0.015953  -10.920864
details:                  WHG    Turkey_Boncuklu_N    -0.010342   -6.587571
details:             Turkey_N    Turkey_Boncuklu_N     0.010664    7.728693
dscore:    Turkey_Boncuklu_N f4:     0.000909 Z:     0.674108

details: Russia_Samara_EBA_Yamnaya           Levant_PPN    -0.013995   -9.355710
details:                  WHG           Levant_PPN    -0.011888   -7.758160
details:             Turkey_N           Levant_PPN     0.009763    7.093255
dscore:           Levant_PPN f4:     0.000906 Z:     0.667221

details: Russia_Samara_EBA_Yamnaya      Israel_Natufian    -0.011254   -5.488518
details:                  WHG      Israel_Natufian    -0.007851   -3.648711
details:             Turkey_N      Israel_Natufian     0.008494    4.403457
dscore:      Israel_Natufian f4:     0.001217 Z:     0.638692

details: Russia_Samara_EBA_Yamnaya     Iran_GanjDareh_N     0.004749    3.745552
details:                  WHG     Iran_GanjDareh_N    -0.009194   -6.507243
details:             Turkey_N     Iran_GanjDareh_N    -0.001984   -1.632945
dscore:     Iran_GanjDareh_N f4:    -0.000161 Z:    -0.136284

details: Russia_Samara_EBA_Yamnaya Russia_AfontovaGora3     0.026766   11.265759
details:                  WHG Russia_AfontovaGora3     0.009496    3.682707
details:             Turkey_N Russia_AfontovaGora3    -0.007037   -3.138894
dscore: Russia_AfontovaGora3 f4:     0.004829 Z:     2.178102

details: Russia_Samara_EBA_Yamnaya Serbia_IronGates_Mesolithic     0.004507    3.087822
details:                  WHG Serbia_IronGates_Mesolithic     0.056493   35.432490
details:             Turkey_N Serbia_IronGates_Mesolithic    -0.005539   -3.984981
dscore: Serbia_IronGates_Mesolithic f4:     0.000929 Z:     0.683563

gendstat:             Mbuti.DG                  EHG     1.320
gendstat:             Mbuti.DG                  CHG    -1.032
gendstat:             Mbuti.DG                 ESHG    -0.488
gendstat:             Mbuti.DG    Turkey_Boncuklu_N     0.674
gendstat:             Mbuti.DG           Levant_PPN     0.667
gendstat:             Mbuti.DG      Israel_Natufian     0.639
gendstat:             Mbuti.DG     Iran_GanjDareh_N    -0.136
gendstat:             Mbuti.DG Russia_AfontovaGora3     2.178
gendstat:             Mbuti.DG Serbia_IronGates_Mesolithic     0.684
gendstat:                  EHG                  CHG    -2.361
gendstat:                  EHG                 ESHG    -1.925
gendstat:                  EHG    Turkey_Boncuklu_N    -0.736
gendstat:                  EHG           Levant_PPN    -0.663
gendstat:                  EHG      Israel_Natufian    -0.324
gendstat:                  EHG     Iran_GanjDareh_N    -1.550
gendstat:                  EHG Russia_AfontovaGora3     1.476
gendstat:                  EHG Serbia_IronGates_Mesolithic    -0.885
gendstat:                  CHG                 ESHG     0.717
gendstat:                  CHG    Turkey_Boncuklu_N     1.747
gendstat:                  CHG           Levant_PPN     1.551
gendstat:                  CHG      Israel_Natufian     1.313
gendstat:                  CHG     Iran_GanjDareh_N     1.088
gendstat:                  CHG Russia_AfontovaGora3     2.848
gendstat:                  CHG Serbia_IronGates_Mesolithic     1.735
gendstat:                 ESHG    Turkey_Boncuklu_N     1.111
gendstat:                 ESHG           Levant_PPN     1.132
gendstat:                 ESHG      Israel_Natufian     0.905
gendstat:                 ESHG     Iran_GanjDareh_N     0.336
gendstat:                 ESHG Russia_AfontovaGora3     2.593
gendstat:                 ESHG Serbia_IronGates_Mesolithic     1.209
gendstat:    Turkey_Boncuklu_N           Levant_PPN    -0.002
gendstat:    Turkey_Boncuklu_N      Israel_Natufian     0.161
gendstat:    Turkey_Boncuklu_N     Iran_GanjDareh_N    -0.883
gendstat:    Turkey_Boncuklu_N Russia_AfontovaGora3     1.819
gendstat:    Turkey_Boncuklu_N Serbia_IronGates_Mesolithic     0.018
gendstat:           Levant_PPN      Israel_Natufian     0.166
gendstat:           Levant_PPN     Iran_GanjDareh_N    -0.822
gendstat:           Levant_PPN Russia_AfontovaGora3     1.742
gendstat:           Levant_PPN Serbia_IronGates_Mesolithic     0.018
gendstat:      Israel_Natufian     Iran_GanjDareh_N    -0.696
gendstat:      Israel_Natufian Russia_AfontovaGora3     1.360
gendstat:      Israel_Natufian Serbia_IronGates_Mesolithic    -0.148
gendstat:     Iran_GanjDareh_N Russia_AfontovaGora3     2.404
gendstat:     Iran_GanjDareh_N Serbia_IronGates_Mesolithic     0.896
gendstat: Russia_AfontovaGora3 Serbia_IronGates_Mesolithic    -1.888

worst Z-score with right hand mix
f4(Target, Fit, Base, mix of Right pops;  Z:    -3.543 sum:     1.000
                           EHG   -54.579
                           CHG    61.133
                          ESHG    65.493
             Turkey_Boncuklu_N   -19.356
                    Levant_PPN   -22.325
               Israel_Natufian   -10.167
              Iran_GanjDareh_N    15.413
          Russia_AfontovaGora3   -43.705
   Serbia_IronGates_Mesolithic     9.092

removing /tmp/fsx.2760
oldmode set: terminating
##end of qpAdm:        1.348 seconds cpu        0.000 Mbytes in use

Code:

qpAdm: parameter file: parqpAdmix.txt
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
indivname: Work.ind
snpname: Work.snp
genotypename: Work.geno
basepop: Han.DG
popleft: left.txt
popright: right.txt
inbreed: NO
allsnps: YES
details: YES
##  qpAdm -p parqpAdmix.txt
## qpAdm version: 2050
seed: 2007363432
basepop set: Han.DG
inbreed set NO
tmp: /tmp/fsx.4450

left pops:
             Stefano      1
    Italy_Verona_LIA     16
   Italy_Imperial.SG     35
   Hungary_Langobard     12

right pops:
            Mbuti.DG     10
                 EHG      5
                 CHG      2
                 WHG      4
            Turkey_N     25
                ESHG     10
          Levant_PPN     14
     Israel_Natufian      5
    Iran_GanjDareh_N      8
Russia_AfontovaGora3      1
Serbia_IronGates_Mesolithic     32

codimension 1
f4info:
f4rank: 2 dof:      8 chisq:    15.089 tail:         0.0574365379 dofdiff:     10 chisqdiff:   -15.089 taildiff:                    1
B:
          scale     1.000     1.000
            EHG     1.443     1.031
            CHG    -0.010     0.873
            WHG     1.710    -1.451
       Turkey_N     0.213    -0.838
           ESHG     0.488    -0.187
     Levant_PPN     0.054     0.539
Israel_Natufian     0.122    -0.092
Iran_GanjDareh_N    -0.021     1.997
Russia_AfontovaGora3     1.313     0.882
Serbia_IronGates_Mesolithic     1.722    -0.516
A:
          scale   191.945   976.539
Italy_Verona_LIA     0.643    -0.616
Italy_Imperial.SG    -0.862     0.370
Hungary_Langobard     1.358     1.576


full rank
f4info:
f4rank: 3 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      8 chisqdiff:    15.089 taildiff:         0.0574365379
B:
          scale   330.192   160.886   164.181
            EHG     0.478    -1.428     1.529
            CHG    -1.049    -0.369    -0.187
            WHG     1.618    -1.627     1.305
       Turkey_N    -0.754    -0.772    -0.525
           ESHG     0.126    -0.585     0.327
     Levant_PPN    -0.981    -0.463    -0.255
Israel_Natufian    -0.549    -0.436    -0.196
Iran_GanjDareh_N    -1.144    -0.218     0.159
Russia_AfontovaGora3     1.313    -0.864     1.849
Serbia_IronGates_Mesolithic     1.083    -1.743     1.413
A:
          scale     1.732     1.732     1.732
Italy_Verona_LIA     1.732     0.000     0.000
Italy_Imperial.SG     0.000     1.732     0.000
Hungary_Langobard     0.000     0.000     1.732


best coefficients:     0.465     0.462     0.073
totmean:      0.465     0.462     0.073
zzevarboot
    0.613122710     0.371310596     0.015566694
    0.002705131    -0.000639406
   -0.004746560     0.000999248
    0.006672632     0.001349206
zzevarboot2
    0.329188571     0.541284222     0.129527207
    0.003852340    -0.000838923
   -0.004154070     0.000160643
    0.007568962     0.001460778
boot mean:     0.467     0.462     0.071
bootstrap saimpling of F-coeffs: 1000
zzjmean     0.467     0.462     0.071
      std. errors:     0.157     0.070     0.117

error covariance (* 1,000,000)
     24771      -8041     -16730
     -8041       4933       3108
    -16730       3108      13622


summ: Stefano    3      0.057437     0.467     0.462     0.071      24771      -8041     -16730       4933       3108   ...
     13622

    fixed pat  wt  dof     chisq       tail prob
          000  0     8    15.089       0.0574365     0.465     0.462     0.073
          001  1     9    15.756       0.0721479     0.556     0.444     0.000
          010  1     9    55.867     8.32361e-09     1.306     0.000    -0.306  infeasible
          100  1     9    23.955      0.00437272     0.000     0.611     0.389
          011  2    10    63.056     9.52791e-10     1.000     0.000     0.000
          101  2    10    88.324     1.15035e-14     0.000     1.000     0.000
          110  2    10   177.595               0     0.000     0.000     1.000
best pat:          000        0.0574365              -  -
best pat:          100       0.00437272  chi(nested):     8.866 p-value for nested model:      0.00290512
best pat:          011      9.52791e-10 not nested

coeffs:     0.465     0.462     0.073

## dscore:: f_4(Base, Fit, Rbase, right2)
## genstat:: f_4(Base, Fit, right1, right2)

details:     Italy_Verona_LIA                  EHG     0.001448    1.003195
details:    Italy_Imperial.SG                  EHG    -0.008878   -6.215792
details:    Hungary_Langobard                  EHG     0.009311    6.395817
dscore:                  EHG f4:    -0.002750 Z:    -1.950686

details:     Italy_Verona_LIA                  CHG    -0.003176   -2.132666
details:    Italy_Imperial.SG                  CHG    -0.002296   -1.524077
details:    Hungary_Langobard                  CHG    -0.001137   -0.729641
dscore:                  CHG f4:    -0.002621 Z:    -1.775883

details:     Italy_Verona_LIA                  WHG     0.004900    3.299876
details:    Italy_Imperial.SG                  WHG    -0.010114   -6.848169
details:    Hungary_Langobard                  WHG     0.007947    5.289474
dscore:                  WHG f4:    -0.001817 Z:    -1.247297

details:     Italy_Verona_LIA             Turkey_N    -0.002283   -2.065800
details:    Italy_Imperial.SG             Turkey_N    -0.004801   -4.304503
details:    Hungary_Langobard             Turkey_N    -0.003198   -2.782188
dscore:             Turkey_N f4:    -0.003514 Z:    -3.215169

details:     Italy_Verona_LIA                 ESHG     0.000383    0.340282
details:    Italy_Imperial.SG                 ESHG    -0.003636   -3.233681
details:    Hungary_Langobard                 ESHG     0.001993    1.774249
dscore:                 ESHG f4:    -0.001357 Z:    -1.232747

details:     Italy_Verona_LIA           Levant_PPN    -0.002971   -2.153003
details:    Italy_Imperial.SG           Levant_PPN    -0.002879   -2.095065
details:    Hungary_Langobard           Levant_PPN    -0.001554   -1.114981
dscore:           Levant_PPN f4:    -0.002825 Z:    -2.085862

details:     Italy_Verona_LIA      Israel_Natufian    -0.001664   -0.838775
details:    Italy_Imperial.SG      Israel_Natufian    -0.002712   -1.390892
details:    Hungary_Langobard      Israel_Natufian    -0.001193   -0.604499
dscore:      Israel_Natufian f4:    -0.002114 Z:    -1.095678

details:     Italy_Verona_LIA     Iran_GanjDareh_N    -0.003465   -2.939604
details:    Italy_Imperial.SG     Iran_GanjDareh_N    -0.001357   -1.167068
details:    Hungary_Langobard     Iran_GanjDareh_N     0.000968    0.800455
dscore:     Iran_GanjDareh_N f4:    -0.002167 Z:    -1.881145

details:     Italy_Verona_LIA Russia_AfontovaGora3     0.003976    1.792318
details:    Italy_Imperial.SG Russia_AfontovaGora3    -0.005369   -2.406227
details:    Hungary_Langobard Russia_AfontovaGora3     0.011259    4.887681
dscore: Russia_AfontovaGora3 f4:     0.000189 Z:     0.086182

details:     Italy_Verona_LIA Serbia_IronGates_Mesolithic     0.003279    2.428296
details:    Italy_Imperial.SG Serbia_IronGates_Mesolithic    -0.010834   -8.029272
details:    Hungary_Langobard Serbia_IronGates_Mesolithic     0.008608    6.257959
dscore: Serbia_IronGates_Mesolithic f4:    -0.002855 Z:    -2.150311

gendstat:             Mbuti.DG                  EHG    -1.951
gendstat:             Mbuti.DG                  CHG    -1.776
gendstat:             Mbuti.DG                  WHG    -1.247
gendstat:             Mbuti.DG             Turkey_N    -3.215
gendstat:             Mbuti.DG                 ESHG    -1.233
gendstat:             Mbuti.DG           Levant_PPN    -2.086
gendstat:             Mbuti.DG      Israel_Natufian    -1.096
gendstat:             Mbuti.DG     Iran_GanjDareh_N    -1.881
gendstat:             Mbuti.DG Russia_AfontovaGora3     0.086
gendstat:             Mbuti.DG Serbia_IronGates_Mesolithic    -2.150
gendstat:                  EHG                  CHG     0.087
gendstat:                  EHG                  WHG     0.718
gendstat:                  EHG             Turkey_N    -0.644
gendstat:                  EHG                 ESHG     1.126
gendstat:                  EHG           Levant_PPN    -0.050
gendstat:                  EHG      Israel_Natufian     0.306
gendstat:                  EHG     Iran_GanjDareh_N     0.434
gendstat:                  EHG Russia_AfontovaGora3     1.477
gendstat:                  EHG Serbia_IronGates_Mesolithic    -0.095
gendstat:                  CHG                  WHG     0.505
gendstat:                  CHG             Turkey_N    -0.685
gendstat:                  CHG                 ESHG     0.894
gendstat:                  CHG           Levant_PPN    -0.129
gendstat:                  CHG      Israel_Natufian     0.239
gendstat:                  CHG     Iran_GanjDareh_N     0.345
gendstat:                  CHG Russia_AfontovaGora3     1.253
gendstat:                  CHG Serbia_IronGates_Mesolithic    -0.162
gendstat:                  WHG             Turkey_N    -1.525
gendstat:                  WHG                 ESHG     0.353
gendstat:                  WHG           Levant_PPN    -0.718
gendstat:                  WHG      Israel_Natufian    -0.148
gendstat:                  WHG     Iran_GanjDareh_N    -0.254
gendstat:                  WHG Russia_AfontovaGora3     0.919
gendstat:                  WHG Serbia_IronGates_Mesolithic    -1.385
gendstat:             Turkey_N                 ESHG     2.089
gendstat:             Turkey_N           Levant_PPN     0.694
gendstat:             Turkey_N      Israel_Natufian     0.791
gendstat:             Turkey_N     Iran_GanjDareh_N     1.333
gendstat:             Turkey_N Russia_AfontovaGora3     1.784
gendstat:             Turkey_N Serbia_IronGates_Mesolithic     0.704
gendstat:                 ESHG           Levant_PPN    -1.153
gendstat:                 ESHG      Israel_Natufian    -0.388
gendstat:                 ESHG     Iran_GanjDareh_N    -0.731
gendstat:                 ESHG Russia_AfontovaGora3     0.751
gendstat:                 ESHG Serbia_IronGates_Mesolithic    -1.270
gendstat:           Levant_PPN      Israel_Natufian     0.376
gendstat:           Levant_PPN     Iran_GanjDareh_N     0.499
gendstat:           Levant_PPN Russia_AfontovaGora3     1.345
gendstat:           Levant_PPN Serbia_IronGates_Mesolithic    -0.024
gendstat:      Israel_Natufian     Iran_GanjDareh_N    -0.026
gendstat:      Israel_Natufian Russia_AfontovaGora3     0.874
gendstat:      Israel_Natufian Serbia_IronGates_Mesolithic    -0.380
gendstat:     Iran_GanjDareh_N Russia_AfontovaGora3     1.140
gendstat:     Iran_GanjDareh_N Serbia_IronGates_Mesolithic    -0.559
gendstat: Russia_AfontovaGora3 Serbia_IronGates_Mesolithic    -1.472

worst Z-score with right hand mix
f4(Target, Fit, Base, mix of Right pops;  Z:    -3.852 sum:     1.000
                           EHG     0.254
                           CHG     0.060
                           WHG    -0.692
                      Turkey_N     1.268
                          ESHG    -0.218
                    Levant_PPN    -0.009
               Israel_Natufian    -0.026
              Iran_GanjDareh_N     0.101
          Russia_AfontovaGora3    -0.268
   Serbia_IronGates_Mesolithic     0.531

removing /tmp/fsx.4450
oldmode set: terminating
##end of qpAdm:        1.673 seconds cpu        0.000 Mbytes in use

Could you link that site? I’m definitely interested in trying it out.

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