Admixtools admixtools2 TUTORIAL for WINDOWS.

[Jalisciense]

Yes. Version 8.0 is the latest so best to download that one from your link and follow the instructions to compile. If you run into trouble you can try some pre-compiled older versions: https://github.com/chrchang/eigensoft

Thanks bro, when I have a chance I'll try it, but I have a question.

Are those the steps where users got a massive geno document x4 size when convert back to Eigenstrat from Plink? And people reporting problems and being not able to do it, so they prefer move to AdmixTools2? That's way you don't need to convert the AADR?

 

[Jovialis]

Here are the steps to merge your sample with AADR, with more clarity:

# Step 1: Convert the 23andMe file to PLINK binary format
plink --23file /path/to/Jovialis_23andMe_file.txt --make-bed --out /path/to/Jovialis_sorted_marked

# Step 2a: Extract SNPs from the Jovialis dataset
plink --bfile /path/to/Jovialis_sorted_marked --write-snplist --allow-no-sex --out /path/to/jovialis_snp_list

# Step 2b: Extract SNPs from the AADR dataset
plink --bfile /path/to/AADR_dataset --write-snplist --allow-no-sex --out /path/to/aadr_snp_list

# Step 3: Find common SNPs between the two datasets (Jovialis and AADR)
comm -12 <(sort /path/to/jovialis_snp_list.snplist) <(sort /path/to/aadr_snp_list.snplist) > /path/to/common_snps.txt

# Step 4: Filter the Jovialis dataset to keep only SNPs present in both datasets (common SNPs)
plink --allow-no-sex --bfile /path/to/Jovialis_sorted_marked --extract /path/to/common_snps.txt --make-bed --out /path/to/Jovialis_common_snps

# Step 5: Attempt an initial merge and identify problematic SNPs (multiallelic or inconsistent strand)
plink --allow-no-sex --bfile /path/to/AADR_dataset --bmerge /path/to/Jovialis_common_snps --make-bed --out /path/to/merged_initial

# Step 6: Flip problematic SNPs in the Jovialis dataset (fix strand inconsistencies)
plink --allow-no-sex --bfile /path/to/Jovialis_common_snps --flip /path/to/merged_initial-merge.missnp --make-bed --out /path/to/Jovialis_flipped

# Step 7: Exclude remaining problematic SNPs from the Jovialis dataset
plink --allow-no-sex --bfile /path/to/Jovialis_flipped --exclude /path/to/merged_initial-merge.missnp --make-bed --out /path/to/Jovialis_filtered

# Step 9: Perform the final merge
plink --allow-no-sex --bfile /path/to/AADR_dataset --bmerge /path/to/Jovialis_filtered --indiv-sort 0 --make-bed --out /path/to/final_merged_dataset

# Step 10a: Check SNP frequency in the final merged dataset
plink --allow-no-sex --bfile /path/to/final_merged_dataset --freq --out /path/to/merged_freq

# Step 10b: Check SNP frequency in the original AADR dataset
plink --allow-no-sex --bfile /path/to/AADR_dataset --freq --out /path/to/aadr_freq

 

[Celtion]

Thanks bro, when I have a chance I'll try it, but I have a question.

Are those the steps where users got a massive geno document x4 size when convert back to Eigenstrat from Plink? And people reporting problems and being not able to do it, so they prefer move to AdmixTools2? That's way you don't need to convert the AADR?

Technically, AADR downloads are in PackedAncestryMap format – not Eigenstrat. So when you use convertf to convert the AADR files to Plink (aka PackedPed) you are converting from PAM, not Eigenstrat. And when users decide to convert "back to Eigenstrat" they are in actuality converting to it for the first time and are surprised at the humungous file size.

To explain further, both Eigestrat and PAM formats use the same file suffixes – .geno, .snp and .ind – but the only difference is with the .geno file. PackedAncestryMap format uses a binary-encoded .geno file which is why it is the same size as the binary-encoded PackedPed (aka Plink) .bed file. The Eigenstrat .geno is not binary encoded and is about 4x the size.

If you are using AdmixTools(1/2) there is no need to convert to Plink format. It is much easier to merge your data in PAM/Eigenstrat format using MergeIt that comes with Eigensoft. MergeIt by default will output as a new file all the intersected snps between the two input files as well as deal with any strand/allele flipping and other issues which can are more of a complicated process with merging in Plink. I compared both methods, merging my dna file with the AADR v62 datasets. The only difference was that MergeIt found a problematic ancient individual in the AADR which it automatically expelled from the merge. Everything else was uniform but MergeIt was much quicker to use.

So you best use convertf to convert your individual Plink file to either PackedAncestryMap or Eigenstrat format. Then use MergeIt to merge it with the AADR setting the output to either PAM (or Eigenstrat if you want a much larger file, lol). Also, Eigenstrat and PAM will merge together fine so it's more the output format which you specify.

 

[ulasn]

A quick guide:

Here’s a detailed guide to subsetting a dataset and performing PCA using SmartPCA (from ADMIXTOOLS):

### **Step 1: Prepare Your Files**
Ensure you have the following files:
1. **`.geno`** file: Contains genotype data.
2. **`.snp`** file: Contains SNP information (chromosome, position, etc.).
3. **`.ind`** file: Contains individual IDs and population assignments.
4. **`Sample_List.txt`**: List of populations or individuals to include in the subset.

---

### **Step 2: Create the Subset**
To create a subset of your dataset, follow these steps:

#### **2.1. Create a `par` file for conversion**
This file specifies the input and output for subsetting. Example `par` file:

```
genotypename:    /path/to/original.geno
snpname:         /path/to/original.snp
indivname:       /path/to/original.ind
outputformat:    EIGENSTRAT
genotypeoutname: /path/to/subset.geno
snpoutname:      /path/to/subset.snp
indivoutname:    /path/to/subset.ind
poplistname:     /path/to/Sample_List.txt
```

#### **2.2. Run `convertf` to create the subset**
Use the following command to run the conversion:

```bash
convertf -p /path/to/par.file
```

---

### **Step 3: Run PCA with SmartPCA**

#### **3.1. Create the SmartPCA `par` file**
This file contains parameters for PCA analysis. Example `par` file:

```
genotypename:    /path/to/subset.geno
snpname:         /path/to/subset.snp
indivname:       /path/to/subset.ind
evecoutname:     /path/to/projected.evec.txt
evaloutname:     /path/to/projected.eval.txt
lsqproject:      YES
numoutevec:      10
poplistname:     /path/to/Sample_List.txt
```

- **`evecoutname`**: Output eigenvectors.
- **`evaloutname`**: Output eigenvalues.
- **`lsqproject`**: Projects individuals onto principal components.
- **`numoutevec`**: Number of principal components to output.

#### **3.2. Run SmartPCA**
Execute the following command:

```bash
smartpca -p /path/to/smartpca.params.txt > /path/to/smartpca.log
```

---

### **Step 4: Analyze and Visualize the PCA Results in R**

Once SmartPCA completes, use the generated `.evec` and `.eval` files for visualization.

#### **4.1. Load Required Libraries**
```r
library(ggplot2)
library(dplyr)
```

#### **4.2. Load Eigenvalues and Eigenvectors**
```r
# Set working directory
setwd("/path/to/output/files")

# Read the eigenvalues
evals <- scan("projected.eval.txt")

# Read the eigenvectors
evecs <- read.table("projected.evec.txt", header = FALSE, stringsAsFactors = FALSE)

# Extract individual IDs and population labels
individuals <- evecs$V1
populations <- evecs$V12  # Adjust if necessary
```

#### **4.3. Plot PCA in R**
```r
# Extract PCs
pc1 <- evecs$V2
pc2 <- evecs$V3

# Create data frame
pca_data <- data.frame(Individual = individuals, Population = populations, PC1 = pc1, PC2 = pc2)

# Plot
ggplot(pca_data, aes(x = PC1, y = PC2, color = Population)) +
  geom_point(size = 2) +
  labs(
    title = "PCA Projection",
    x = paste0("PC1 (", round(evals[1] / sum(evals) * 100, 2), "% variance)"),
    y = paste0("PC2 (", round(evals[2] / sum(evals) * 100, 2), "% variance)")
  ) +
  theme_minimal()
```

---

### **Summary of Commands**
1. **Subsetting**:
   ```bash
   convertf -p /path/to/par.file
   ```

2. **Run PCA**:
   ```bash
   smartpca -p /path/to/smartpca.params.txt > /path/to/smartpca.log
   ```

3. **Visualize in R**:
   Follow the provided R script to load and plot the results.

Good Guide. But, I can't run smartpca, I got this error:
Do you know how to solve it?

 

[Jalisciense]

Technically, AADR downloads are in PackedAncestryMap format – not Eigenstrat. So when you use convertf to convert the AADR files to Plink (aka PackedPed) you are converting from PAM, not Eigenstrat. And when users decide to convert "back to Eigenstrat" they are in actuality converting to it for the first time and are surprised at the humungous file size.

To explain further, both Eigestrat and PAM formats use the same file suffixes – .geno, .snp and .ind – but the only difference is with the .geno file. PackedAncestryMap format uses a binary-encoded .geno file which is why it is the same size as the binary-encoded PackedPed (aka Plink) .bed file. The Eigenstrat .geno is not binary encoded and is about 4x the size.

If you are using AdmixTools(1/2) there is no need to convert to Plink format. It is much easier to merge your data in PAM/Eigenstrat format using MergeIt that comes with Eigensoft. MergeIt by default will output as a new file all the intersected snps between the two input files as well as deal with any strand/allele flipping and other issues which can are more of a complicated process with merging in Plink. I compared both methods, merging my dna file with the AADR v62 datasets. The only difference was that MergeIt found a problematic ancient individual in the AADR which it automatically expelled from the merge. Everything else was uniform but MergeIt was much quicker to use.

So you best use convertf to convert your individual Plink file to either PackedAncestryMap or Eigenstrat format. Then use MergeIt to merge it with the AADR setting the output to either PAM (or Eigenstrat if you want a much larger file, lol). Also, Eigenstrat and PAM will merge together fine so it's more the output format which you specify.

Thanks for the good reply bro.

I think I'm going to install AdmixTools2 too, do you know if I could do if my current R studio v 4.3.3? Or does it have to be a particular version? And what about R tools? Can the newest version be downloaded?

 

[baeticvs]

Thanks for the good reply bro.

I think I'm going to install AdmixTools2 too, do you know if I could do if my current R studio v 4.3.3? Or does it have to be a particular version? And what about R tools? Can the newest version be downloaded?

it doesnt have to be any particular version, im using the latest one (4.4.2) and it works just fine

 

[Celtion]

Thanks for the good reply bro.

I think I'm going to install AdmixTools2 too, do you know if I could do if my current R studio v 4.3.3? Or does it have to be a particular version? And what about R tools? Can the newest version be downloaded?

Latest version should be fine. Remember to first install latest version of R, and then R Studio. I use a Mac so there's no R Tools for me as it's Windows only. But as with the others I would recommend downloading the latest version.

 

[Jalisciense]

it doesnt have to be any particular version, im using the latest one (4.4.2) and it works just fine
View attachment 17052

Nice bro, thanks! I asked because I read here somewhere that wasn't sure if it'd work in a newer R studio version, but you confirmed that It can.

 

[Jalisciense]

Latest version should be fine. Remember to first install latest version of R, and then R Studio. I use a Mac so there's no R Tools for me as it's Windows only. But as with the others I would recommend downloading the latest version.

Ok! I'll have to update it then.

Btw maybe a dumb question bro, but it could be possible to merge a raw data to AADR if you just download Plink and the AADR without having to install any AdmixTools?

 

[Celtion]

Ok! I'll have to update it then.

Btw maybe a dumb question bro, but it could be possible to merge a raw data to AADR if you just download Plink and the AADR without having to install any AdmixTools?

Yes, the merging is done in either mergeit or Plink and is not dependent on AT. I would strongly recommend mergeit though as the Plink merge process is more complicated.

 

[Jalisciense]

Okay I see the problem now. In your working directory it looks like you only have v62.0_1240k_public in PACKEDANCESTRYMAP format (similar to Eigenstrat). You need to convert it to PACKEDPED (Plink format) using ConvertF so you have the .bed, .bim and .fam files.

I did what you told me in this post yours ^

(I'm still using AdmixTools1 btw).

And I used the command:

convertf -p par.EIGENSTRAT.PED

Then I got this:

jalisciense@vbox:~> cd bin
jalisciense@vbox:~/bin> convertf -p par.EIGENSTRAT.PED
parameter file: par.EIGENSTRAT.PED
genotypename: v62.0_1240k_public.geno
snpname: v62.0_1240k_public.snp
indivname: v62.0_1240k_public.ind
outputformat: PACKEDPED
genotypeoutname: v62_1240k.bed
snpoutname: v62_1240k.bim
indivoutname: v62_1240k.fam
## convertf version: 8600
read 1073741824 bytes
read 2147483648 bytes
read 3221225472 bytes
read 4294967296 bytes
read 5368709120 bytes
read 5435121304 bytes
packed geno read OK
end of inpack
before compress: snps: 1233013 indivs: 17629
after compress: snps: 1233013 indivs: 17629

It's all? Because it seems it's not finished (there is no new file in the folder) or is it normal that is taking forever? (it has passed like 15 minutes).

 

[Jalisciense]

Technically, AADR downloads are in PackedAncestryMap format – not Eigenstrat. So when you use convertf to convert the AADR files to Plink (aka PackedPed) you are converting from PAM, not Eigenstrat. And when users decide to convert "back to Eigenstrat" they are in actuality converting to it for the first time and are surprised at the humungous file size.

To explain further, both Eigestrat and PAM formats use the same file suffixes – .geno, .snp and .ind – but the only difference is with the .geno file. PackedAncestryMap format uses a binary-encoded .geno file which is why it is the same size as the binary-encoded PackedPed (aka Plink) .bed file. The Eigenstrat .geno is not binary encoded and is about 4x the size.

If you are using AdmixTools(1/2) there is no need to convert to Plink format. It is much easier to merge your data in PAM/Eigenstrat format using MergeIt that comes with Eigensoft. MergeIt by default will output as a new file all the intersected snps between the two input files as well as deal with any strand/allele flipping and other issues which can are more of a complicated process with merging in Plink. I compared both methods, merging my dna file with the AADR v62 datasets. The only difference was that MergeIt found a problematic ancient individual in the AADR which it automatically expelled from the merge. Everything else was uniform but MergeIt was much quicker to use.

So you best use convertf to convert your individual Plink file to either PackedAncestryMap or Eigenstrat format. Then use MergeIt to merge it with the AADR setting the output to either PAM (or Eigenstrat if you want a much larger file, lol). Also, Eigenstrat and PAM will merge together fine so it's more the output format which you specify.

The conversion of AADR to "Plink" was taking so long, so I tried instead convert my .bed, .bim and .fam files of mydata to PackedAncestryMap and they were converted successfully to .geno, .snp and .ind with a file named par.PACKEDPED.PACKEDANCESTRYMAP with this inside:

genotypename: mydata.bed
snpname: mydata.bim
indivname: mydata.fam
outputformat: PACKEDANCESTRYMAP
genotypeoutname: mydata.geno
snpoutname: mydata.snp
indivoutname: mydata.ind
familynames: NO

So I run this command:

convertf -p- par.PACKEDPED.PACKEDANCESTRYMAP

I received my .geno, .snp and .ind files

So I tried to merge them to the AADR .geno, .snp and .ind, I made myself (Because I didn't find the file in the Convertf folder) a file named merge_param.par with this inside:

geno1: v62.0_1240k_public.geno

snp1: v62.0_1240k_public.snp

ind1: v62.0_1240k_public.ind

geno2: mydata.geno

snp2: mydata.snp

ind2: mydata.ind

genooutfilename: mydata_merged_with_1240k.geno

snpoutfilename: mydata_merged_with_1240k.snp

indoutfilename: mydata_merged_with_1240k.ind


outputformat: PACKEDANCESTRYMAP


Then I run it with this command:

mergeit -p merge_param.par

And I received this:

 

[Jalisciense]

jalisciense@vbox:~/bin> mergeit -p merge_param.par
parameter file: merge_param.par
geno1: v62.0_1240k_public.geno
snp1: v62.0_1240k_public.snp
ind1: v62.0_1240k_public.ind
geno2: mydata.geno
snp2: mydata.snp
ind2: mydata.ind
genooutfilename: mydata_merged_with_1240k.geno
snpoutfilename: mydata_merged_with_1240k.snp
indoutfilename: mydata_merged_with_1240k.ind
outputformat: PACKEDANCESTRYMAP
## mergeit version: 3130
allele funny: rs2679218 T C X X
allele funny: rs7418365 A G X X
allele funny: rs2495090 C T X X
allele funny: rs6686602 G T X X
allele funny: rs97922 T G X X
allele funny: rs9645433 A G X X
allele funny: rs6678619 G A X X
allele funny: rs2149116 G A X X
allele funny: rs12097924 G T X X
allele funny: rs12566647 G A X X
allele funny: rs1772782 A G X X
allele funny: rs2391467 A G X X
allele funny: rs2222748 T C X X
allele funny: rs2064901 A G X X
allele funny: rs6694580 G T X X
allele funny: rs1130183 G A X X
allele funny: rs1409814 A G X X
allele funny: rs2181289 T C X X
allele funny: rs1875431 C T X X
allele funny: rs664855 T C X X
allele funny: rs789358 T G X X
allele funny: rs6698720 G T X X
allele funny: rs6586393 A C X X
allele funny: rs4853896 T C X X
allele funny: rs16866330 G T X X
allele funny: rs1881394 G A X X
allele funny: rs6742561 A G X X
allele funny: rs6717847 G T X X
allele funny: rs971732 A C X X
allele funny: rs3796008 G A X X
allele funny: rs11126264 G A X X
allele funny: rs971121 C A X X
allele funny: rs747078 A C X X
allele funny: rs1254900 A G X X
allele funny: rs7422930 C A X X
allele funny: rs951774 C A X X
allele funny: rs72941970 A C X X
allele funny: rs3789117 T C X X
allele funny: rs2863960 G A X X
allele funny: rs1430090 A C X X
allele funny: rs4668168 G A X X
allele funny: rs13384346 T G X X
allele funny: rs821147 T C X X
allele funny: rs16858808 G A X X
allele funny: rs10932806 G A X X
allele funny: rs6719473 G T X X
allele funny: rs2396499 T C X X
allele funny: rs4233617 G T X X
allele funny: rs6437332 C T X X
allele funny: rs2648573 C T X X
allele funny: rs1157564 A G X X
allele funny: rs11129178 T C X X
allele funny: rs9825633 C T X X
allele funny: rs7647242 C T X X
allele funny: rs1501187 T C X X
allele funny: rs3772424 C T X X
allele funny: rs16852884 T C X X
allele funny: rs2724693 G A X X
allele funny: rs4894409 A G X X
allele funny: rs12496761 C T X X
allele funny: rs892761 G T X X
allele funny: rs1003995 C A X X
allele funny: rs1203111 G A X X
allele funny: rs10805327 A C X X
allele funny: rs17603961 G T X X
allele funny: rs11728461 A G X X
allele funny: rs4493603 C T X X
allele funny: rs17010313 A G X X
allele funny: rs4611932 G A X X
allele funny: rs6828433 G A X X
allele funny: rs4253418 A G X X
allele funny: rs11738699 G A X X
allele funny: rs16884543 A G X X
allele funny: rs11750498 T G X X
allele funny: rs7714333 A G X X
allele funny: rs13175997 T C X X
allele funny: rs6875503 A G X X
allele funny: rs1532122 G T X X
allele funny: rs234687 A G X X
allele funny: rs6453423 G A X X
allele funny: rs3885676 T C X X
allele funny: rs2784956 C T X X
allele funny: rs2496302 A C X X
allele funny: rs316338 A G X X
allele funny: rs6910086 T C X X
allele funny: rs9460965 C T X X
allele funny: rs2267641 A C X X
allele funny: rs2074489 C T X X
allele funny: rs9275330 A G X X
allele funny: rs2071482 C A X X
allele funny: rs3135024 T C X X
allele funny: rs12529592 G T X X
allele funny: rs6926332 A C X X
allele funny: rs4286803 T C X X
allele funny: rs10945657 T G X X
allele funny: rs7752540 C T X X
allele funny: rs7772901 A C X X
allele funny: rs1976134 T G X X
allele funny: rs907719 C A X X
allele funny: rs11771147 G A X X
allele funny: rs17153994 T C X X
allele funny: rs12699609 C T X X
allele funny: rs2069835 T C X X
allele funny: rs17147385 C A X X
allele funny: rs6954013 A C X X
allele funny: rs2862880 A G X X
allele funny: rs2856728 C T X X
allele funny: rs73137125 A G X X
allele funny: rs11761151 C A X X
allele funny: rs1861381 A G X X
allele funny: rs2075672 A G X X
allele funny: rs965003 C T X X
allele funny: rs6953882 G A X X
allele funny: rs1181908 A C X X
allele funny: rs13252487 C A X X
allele funny: rs1043225 C A X X
allele funny: rs7015706 A G X X
allele funny: rs13261141 A G X X
allele funny: rs2736360 G A X X
allele funny: rs10503462 A G X X
allele funny: rs2739679 T C X X
allele funny: rs11136047 A C X X
allele funny: rs2165498 G A X X
allele funny: rs7821477 T C X X
allele funny: rs7845263 C T X X
allele funny: rs7852128 T G X X
allele funny: rs1331226 G T X X
allele funny: rs3739680 T C X X
allele funny: rs7024727 G T X X
allele funny: rs11143948 C T X X
allele funny: rs10992883 C T X X
allele funny: rs12551731 A G X X
allele funny: rs944961 C T X X
allele funny: rs10985112 G A X X
allele funny: rs7037809 C T X X
allele funny: rs10819014 G T X X
allele funny: rs7021965 T C X X
allele funny: rs10993774 A G X X
allele funny: rs4842206 A G X X
allele funny: rs10858365 T C X X
allele funny: rs17578859 G A X X
allele funny: rs728939 C T X X
allele funny: rs2664904 G T X X
allele funny: rs7900357 G A X X
allele funny: rs11015383 T G X X
allele funny: rs4747651 G A X X
allele funny: rs2505629 G A X X
allele funny: rs9422546 T G X X
allele funny: rs7088140 G T X X
allele funny: rs1171655 C T X X
allele funny: rs7090742 G A X X
allele funny: rs288452 G A X X
allele funny: rs1250550 C A X X
allele funny: rs12416404 C T X X
allele funny: rs11814628 G A X X
allele funny: rs11816423 C T X X
allele funny: rs11189692 T C X X
allele funny: rs3120592 C T X X
allele funny: rs17130385 G T X X
allele funny: rs6585256 A C X X
allele funny: rs11593974 T C X X
allele funny: rs12242650 T C X X
allele funny: rs12258833 A G X X
allele funny: rs3095757 A C X X
allele funny: rs163184 T G X X
allele funny: rs7108738 T G X X
allele funny: rs10768001 A G X X
allele funny: rs7925657 A G X X
allele funny: rs11228498 A G X X
allele funny: rs10899446 T C X X
allele funny: rs3750997 A C X X
allele funny: rs616714 G T X X
allele funny: rs2448281 C A X X
allele funny: rs10765800 T C X X
allele funny: rs2887193 G A X X
allele funny: rs11217816 G A X X
allele funny: rs584329 T C X X
allele funny: rs7127978 A C X X
allele funny: rs11062904 G T X X
allele funny: rs3741930 C T X X
allele funny: rs11064391 A C X X
allele funny: rs2160512 A G X X
allele funny: rs12578750 T G X X
allele funny: rs10771783 G A X X
allele funny: rs34546217 C T I D
allele funny: rs1850126 G T X X
allele funny: rs420644 T C X X
allele funny: rs10877902 G T X X
allele funny: rs17110927 T C X X
allele funny: rs7295566 C T X X
allele funny: rs4584620 C T X X
allele funny: rs12828692 G A X X
allele funny: rs1955105 T G X X
allele funny: rs10774563 G A X X
allele funny: rs10847580 G T X X
allele funny: rs10848320 T C X X
allele funny: rs17076896 T C X X
allele funny: rs12584878 C A X X
allele funny: rs9576228 A G X X
allele funny: rs11843185 A G X X
allele funny: rs7338697 A G X X
allele funny: rs622337 A G X X
allele funny: rs9596012 C A X X
allele funny: rs17085643 T C X X
allele funny: rs9602954 T C X X
allele funny: rs12184508 T C X X
allele funny: rs9300812 G A X X
allele funny: rs17176643 C A X X
allele funny: rs2054492 A C X X
allele funny: rs2750131 C A X X
allele funny: rs1876529 A G X X
allele funny: rs7140789 C T X X
allele funny: rs4983590 G A X X
allele funny: rs1863279 T G X X
allele funny: rs2125615 A G X X
allele funny: rs1846135 A G X X
allele funny: rs6494967 G A X X
allele funny: rs2870112 C T X X
allele funny: rs4932432 C A X X
allele funny: rs9920762 T C X X
allele funny: rs2271552 C T X X
allele funny: rs1551990 T C X X
allele funny: rs13330260 C T X X
allele funny: rs11077123 G A X X
allele funny: rs12599790 C A X X


etc etc etc more allele funny: rs ----- etc

fatalx:
* mismatch for SNP rs35182651 24:    21712759 24:    22725065
Aborted (core dumped)

What did I do wrong? What I do and how I fix it?

 

[Jalisciense]

Just in case anyone wants to know, you convert eigenstrat format files to plink by creating a parfile in plink like so (This is also a note for me so I can remember; re-learning this stuff after a year can take a while):

1. Open Ubantu and navigate to where you have it mount, and where you send your files. Ming is on a D drive called "UbuntuJovialisHome":

cd /mnt/d/UbuntuJovialisHome/

2. Create the parfile, I use nano:

nano parfile

3. In the nano file editor type this:

genotypename:    /mnt/d/UbuntuJovialisHome/v62.0_HO_public.geno
snpname:         /mnt/d/UbuntuJovialisHome/v62.0_HO_public.snp
indivname:       /mnt/d/UbuntuJovialisHome/v62.0_HO_public.ind
outputformat:    PACKEDPED
genotypeoutname: /mnt/d/UbuntuJovialisHome/data.bed
snpoutname:      /mnt/d/UbuntuJovialisHome/data.bim
indivoutname:    /mnt/d/UbuntuJovialisHome/data.fam
familynames:     NO

4. Finally, execute the parfile to produce the BED, BIM, and FAM:

convertf -p /mnt/d/UbuntuJovialisHome/parfile

After a while it will finish processing and generate in the destination you are sending it to.

Optional. Here's a quick way to verify in Ubuntu when it is done processing (or you can just navigate there):

ls -lh /mnt/d/UbuntuJovialisHome/v62.0_HO_public.*

How long does it take to convert AADR to Plink? With me, like 10 minutes had passed and it hadn't finished, so I stopped the processing because I thought it had a kind of error or something...

 

[Jovialis]

How long does it take to convert AADR to Plink? With me, like 10 minutes had passed and it hadn't finished, so I stopped the processing because I thought it had a kind of error or something...

It could take like over an hour, don't be discouraged, it may even look frozen, but it is doing the processing. Even if the cursor stops moving.

 

[Celtion]

jalisciense@vbox:~/bin> mergeit -p merge_param.par
parameter file: merge_param.par
geno1: v62.0_1240k_public.geno
snp1: v62.0_1240k_public.snp
ind1: v62.0_1240k_public.ind
geno2: mydata.geno
snp2: mydata.snp
ind2: mydata.ind
genooutfilename: mydata_merged_with_1240k.geno
snpoutfilename: mydata_merged_with_1240k.snp
indoutfilename: mydata_merged_with_1240k.ind
outputformat: PACKEDANCESTRYMAP
## mergeit version: 3130
allele funny: rs2679218 T C X X
allele funny: rs7418365 A G X X
allele funny: rs2495090 C T X X
allele funny: rs6686602 G T X X
allele funny: rs97922 T G X X
allele funny: rs9645433 A G X X
allele funny: rs6678619 G A X X
allele funny: rs2149116 G A X X
allele funny: rs12097924 G T X X
allele funny: rs12566647 G A X X
allele funny: rs1772782 A G X X
allele funny: rs2391467 A G X X
allele funny: rs2222748 T C X X
allele funny: rs2064901 A G X X
allele funny: rs6694580 G T X X
allele funny: rs1130183 G A X X
allele funny: rs1409814 A G X X
allele funny: rs2181289 T C X X
allele funny: rs1875431 C T X X
allele funny: rs664855 T C X X
allele funny: rs789358 T G X X
allele funny: rs6698720 G T X X
allele funny: rs6586393 A C X X
allele funny: rs4853896 T C X X
allele funny: rs16866330 G T X X
allele funny: rs1881394 G A X X
allele funny: rs6742561 A G X X
allele funny: rs6717847 G T X X
allele funny: rs971732 A C X X
allele funny: rs3796008 G A X X
allele funny: rs11126264 G A X X
allele funny: rs971121 C A X X
allele funny: rs747078 A C X X
allele funny: rs1254900 A G X X
allele funny: rs7422930 C A X X
allele funny: rs951774 C A X X
allele funny: rs72941970 A C X X
allele funny: rs3789117 T C X X
allele funny: rs2863960 G A X X
allele funny: rs1430090 A C X X
allele funny: rs4668168 G A X X
allele funny: rs13384346 T G X X
allele funny: rs821147 T C X X
allele funny: rs16858808 G A X X
allele funny: rs10932806 G A X X
allele funny: rs6719473 G T X X
allele funny: rs2396499 T C X X
allele funny: rs4233617 G T X X
allele funny: rs6437332 C T X X
allele funny: rs2648573 C T X X
allele funny: rs1157564 A G X X
allele funny: rs11129178 T C X X
allele funny: rs9825633 C T X X
allele funny: rs7647242 C T X X
allele funny: rs1501187 T C X X
allele funny: rs3772424 C T X X
allele funny: rs16852884 T C X X
allele funny: rs2724693 G A X X
allele funny: rs4894409 A G X X
allele funny: rs12496761 C T X X
allele funny: rs892761 G T X X
allele funny: rs1003995 C A X X
allele funny: rs1203111 G A X X
allele funny: rs10805327 A C X X
allele funny: rs17603961 G T X X
allele funny: rs11728461 A G X X
allele funny: rs4493603 C T X X
allele funny: rs17010313 A G X X
allele funny: rs4611932 G A X X
allele funny: rs6828433 G A X X
allele funny: rs4253418 A G X X
allele funny: rs11738699 G A X X
allele funny: rs16884543 A G X X
allele funny: rs11750498 T G X X
allele funny: rs7714333 A G X X
allele funny: rs13175997 T C X X
allele funny: rs6875503 A G X X
allele funny: rs1532122 G T X X
allele funny: rs234687 A G X X
allele funny: rs6453423 G A X X
allele funny: rs3885676 T C X X
allele funny: rs2784956 C T X X
allele funny: rs2496302 A C X X
allele funny: rs316338 A G X X
allele funny: rs6910086 T C X X
allele funny: rs9460965 C T X X
allele funny: rs2267641 A C X X
allele funny: rs2074489 C T X X
allele funny: rs9275330 A G X X
allele funny: rs2071482 C A X X
allele funny: rs3135024 T C X X
allele funny: rs12529592 G T X X
allele funny: rs6926332 A C X X
allele funny: rs4286803 T C X X
allele funny: rs10945657 T G X X
allele funny: rs7752540 C T X X
allele funny: rs7772901 A C X X
allele funny: rs1976134 T G X X
allele funny: rs907719 C A X X
allele funny: rs11771147 G A X X
allele funny: rs17153994 T C X X
allele funny: rs12699609 C T X X
allele funny: rs2069835 T C X X
allele funny: rs17147385 C A X X
allele funny: rs6954013 A C X X
allele funny: rs2862880 A G X X
allele funny: rs2856728 C T X X
allele funny: rs73137125 A G X X
allele funny: rs11761151 C A X X
allele funny: rs1861381 A G X X
allele funny: rs2075672 A G X X
allele funny: rs965003 C T X X
allele funny: rs6953882 G A X X
allele funny: rs1181908 A C X X
allele funny: rs13252487 C A X X
allele funny: rs1043225 C A X X
allele funny: rs7015706 A G X X
allele funny: rs13261141 A G X X
allele funny: rs2736360 G A X X
allele funny: rs10503462 A G X X
allele funny: rs2739679 T C X X
allele funny: rs11136047 A C X X
allele funny: rs2165498 G A X X
allele funny: rs7821477 T C X X
allele funny: rs7845263 C T X X
allele funny: rs7852128 T G X X
allele funny: rs1331226 G T X X
allele funny: rs3739680 T C X X
allele funny: rs7024727 G T X X
allele funny: rs11143948 C T X X
allele funny: rs10992883 C T X X
allele funny: rs12551731 A G X X
allele funny: rs944961 C T X X
allele funny: rs10985112 G A X X
allele funny: rs7037809 C T X X
allele funny: rs10819014 G T X X
allele funny: rs7021965 T C X X
allele funny: rs10993774 A G X X
allele funny: rs4842206 A G X X
allele funny: rs10858365 T C X X
allele funny: rs17578859 G A X X
allele funny: rs728939 C T X X
allele funny: rs2664904 G T X X
allele funny: rs7900357 G A X X
allele funny: rs11015383 T G X X
allele funny: rs4747651 G A X X
allele funny: rs2505629 G A X X
allele funny: rs9422546 T G X X
allele funny: rs7088140 G T X X
allele funny: rs1171655 C T X X
allele funny: rs7090742 G A X X
allele funny: rs288452 G A X X
allele funny: rs1250550 C A X X
allele funny: rs12416404 C T X X
allele funny: rs11814628 G A X X
allele funny: rs11816423 C T X X
allele funny: rs11189692 T C X X
allele funny: rs3120592 C T X X
allele funny: rs17130385 G T X X
allele funny: rs6585256 A C X X
allele funny: rs11593974 T C X X
allele funny: rs12242650 T C X X
allele funny: rs12258833 A G X X
allele funny: rs3095757 A C X X
allele funny: rs163184 T G X X
allele funny: rs7108738 T G X X
allele funny: rs10768001 A G X X
allele funny: rs7925657 A G X X
allele funny: rs11228498 A G X X
allele funny: rs10899446 T C X X
allele funny: rs3750997 A C X X
allele funny: rs616714 G T X X
allele funny: rs2448281 C A X X
allele funny: rs10765800 T C X X
allele funny: rs2887193 G A X X
allele funny: rs11217816 G A X X
allele funny: rs584329 T C X X
allele funny: rs7127978 A C X X
allele funny: rs11062904 G T X X
allele funny: rs3741930 C T X X
allele funny: rs11064391 A C X X
allele funny: rs2160512 A G X X
allele funny: rs12578750 T G X X
allele funny: rs10771783 G A X X
allele funny: rs34546217 C T I D
allele funny: rs1850126 G T X X
allele funny: rs420644 T C X X
allele funny: rs10877902 G T X X
allele funny: rs17110927 T C X X
allele funny: rs7295566 C T X X
allele funny: rs4584620 C T X X
allele funny: rs12828692 G A X X
allele funny: rs1955105 T G X X
allele funny: rs10774563 G A X X
allele funny: rs10847580 G T X X
allele funny: rs10848320 T C X X
allele funny: rs17076896 T C X X
allele funny: rs12584878 C A X X
allele funny: rs9576228 A G X X
allele funny: rs11843185 A G X X
allele funny: rs7338697 A G X X
allele funny: rs622337 A G X X
allele funny: rs9596012 C A X X
allele funny: rs17085643 T C X X
allele funny: rs9602954 T C X X
allele funny: rs12184508 T C X X
allele funny: rs9300812 G A X X
allele funny: rs17176643 C A X X
allele funny: rs2054492 A C X X
allele funny: rs2750131 C A X X
allele funny: rs1876529 A G X X
allele funny: rs7140789 C T X X
allele funny: rs4983590 G A X X
allele funny: rs1863279 T G X X
allele funny: rs2125615 A G X X
allele funny: rs1846135 A G X X
allele funny: rs6494967 G A X X
allele funny: rs2870112 C T X X
allele funny: rs4932432 C A X X
allele funny: rs9920762 T C X X
allele funny: rs2271552 C T X X
allele funny: rs1551990 T C X X
allele funny: rs13330260 C T X X
allele funny: rs11077123 G A X X
allele funny: rs12599790 C A X X


etc etc etc more allele funny: rs ----- etc

fatalx:
* mismatch for SNP rs35182651 24:    21712759 24:    22725065
Aborted (core dumped)

What did I do wrong? What I do and how I fix it?

The "allele funny" errors usually only occurs if you merge two Plink files in mergeit since they require a more complicated process to flip snps which is done in Plink itself. It shouldn't happen if you merge two PackedAncestryMap or two Eigenstrat files since mergeit by default will check for any strand inconsistencies and flip where necessary.

What version of Eigensoft did you install?
Also open your original raw data file (from whatever testing company) as a text file and check the information at the top. What human assembly build did they use? (e.g. build 37)
Does it mention which strand they reported on? (e.g. forward (+))

 

[Jalisciense]

It could take like over an hour, don't be discouraged, it may even look frozen, but it is doing the processing. Even if the cursor stops moving.

Thanks for the encouragement bro, but it has passed 4 hours, so I'm losing the patience, besides I'm tired and sleepy lol

I downloaded the AADR v62_1240k not the HO version btw.

I'd give some info about my laptop:

I'm using Linux (OpenSuse 15.6) in a virtual machine/box, and I gave it 6100 MB (6.1 GB) of RAM out of 8000 MB (8 GB) and 4 computer processors out of 8.

The processor is Intel ® Core ™ i5-10300H.

Is not enough and failed or is just slower than other computers/laptops? :/

 

[Jalisciense]

The "allele funny" errors usually only occurs if you merge two Plink files in mergeit since they require a more complicated process to flip snps which is done in Plink itself. It shouldn't happen if you merge two PackedAncestryMap or two Eigenstrat files since mergeit by default will check for any strand inconsistencies and flip where necessary.

What version of Eigensoft did you install?
Also open your original raw data file (from whatever testing company) as a text file and check the information at the top. What human assembly build did they use? (e.g. build 37)
Does it mention which strand they reported on? (e.g. forward (+))

As you see bro, I converted them to PackedAncestryMap, I did it again, this time I downloaded and installed this Eigentools (The one you recommended me):

GitHub - DReichLab/EIG: Eigen tools by Nick Patterson and Alkes Price lab

Eigen tools by Nick Patterson and Alkes Price lab. Contribute to DReichLab/EIG development by creating an account on GitHub.

github.com

And I run it:

jalisciense@vbox:~> cd Downloads
jalisciense@vbox:~/Downloads> ls
AdmixTools EIG-master EIG-master.zip plink_linux_x86_64_20241022
jalisciense@vbox:~/Downloads> cd EIG-master
jalisciense@vbox:~/Downloads/EIG-master> cd src
jalisciense@vbox:~/Downloads/EIG-master/src> make
cc -I../include -I/usr/include/openblas -c -o baseprog.o baseprog.c
cc -I../include -I/usr/include/openblas -c -o mcio.o mcio.c
cc -I../include -I/usr/include/openblas -c -o egsubs.o egsubs.c
cc -I../include -I/usr/include/openblas -c -o admutils.o admutils.c
cc -I../include -I/usr/include/openblas -c -o h2d.o h2d.c
cc -I../include -I/usr/include/openblas -c -o eigensrc/exclude.o eigensrc/exclude.c
make -C nicksrc
make[1]: Entering directory '/home/jalisciense/Downloads/EIG-master/src/nicksrc'
cc -c -O3 -g -p -Wimplicit -I../../include -c -o strsubs.o strsubs.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o sortit.o sortit.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o vsubs.o vsubs.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o statsubs.o statsubs.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o linsubs.o linsubs.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o getpars.o getpars.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o xsearch.o xsearch.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o gauss.o gauss.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o gds.o gds.c
ar -r libnick.a strsubs.o sortit.o vsubs.o statsubs.o linsubs.o getpars.o xsearch.o gauss.o gds.o
ar: creating libnick.a
ranlib libnick.a
make[1]: Leaving directory '/home/jalisciense/Downloads/EIG-master/src/nicksrc'
cc baseprog.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o baseprog
cc -I../include -I/usr/include/openblas -c -o convertf.o convertf.c
cc convertf.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o convertf
cc -I../include -I/usr/include/openblas -c -o mergeit.o mergeit.c
cc mergeit.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o mergeit
cc -I../include -I/usr/include/openblas -c -o pca.o pca.c
cc -I../include -I/usr/include/openblas -c -o eigensrc/eigsubs.o eigensrc/eigsubs.c
cc -I../include -I/usr/include/openblas -c -o eigensrc/eigx.o eigensrc/eigx.c
cc pca.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o pca
cc -I../include -I/usr/include/openblas -c -o eigensrc/pcatoy.o eigensrc/pcatoy.c
cc eigensrc/pcatoy.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o eigensrc/pcatoy
cc -I../include -I/usr/include/openblas -c -o eigensrc/smartrel.o eigensrc/smartrel.c
cc -I../include -I/usr/include/openblas -c -o twsubs.o twsubs.c
cc -I../include -I/usr/include/openblas -c -o qpsubs.o qpsubs.c
cc -I../include -I/usr/include/openblas -c -o regsubs.o regsubs.c
cc -I../include -I/usr/include/openblas -c -o eigensrc/smartsubs.o eigensrc/smartsubs.c
cc eigensrc/smartrel.o twsubs.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o eigensrc/eigsubs.o eigensrc/eigx.o eigensrc/smartsubs.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o eigensrc/smartrel
cc -I../include -I/usr/include/openblas -c -o eigensrc/smarteigenstrat.o eigensrc/smarteigenstrat.c
cc eigensrc/smarteigenstrat.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o eigensrc/smarteigenstrat
cc -I../include -I/usr/include/openblas -c -o eigensrc/twstats.o eigensrc/twstats.c
cc eigensrc/twstats.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o eigensrc/twstats
cc -I../include -I/usr/include/openblas eigensrc/eigenstrat.c -lgsl -lopenblas -lm -lpthread -o eigensrc/eigenstrat
cc -I../include -I/usr/include/openblas eigensrc/eigenstratQTL.c -lgsl -lopenblas -lm -lpthread -o eigensrc/eigenstratQTL
cc -I../include -I/usr/include/openblas -c -o eigensrc/smartpca.o eigensrc/smartpca.c
cc -I../include -I/usr/include/openblas -c -o gval.o gval.c
cc -I../include -I/usr/include/openblas -c -o ksrc/kjg_fpca.o ksrc/kjg_fpca.c
cc -I../include -I/usr/include/openblas -c -o ksrc/kjg_gsl.o ksrc/kjg_gsl.c
cc eigensrc/smartpca.o eigensrc/eigsubs.o eigensrc/exclude.o eigensrc/smartsubs.o eigensrc/eigx.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o gval.o nicksrc/libnick.a ksrc/kjg_fpca.o ksrc/kjg_gsl.o -lgsl -lopenblas -lm -lpthread -o eigensrc/smartpca
jalisciense@vbox:~/Downloads/EIG-master/src> make install
mv baseprog convertf mergeit pca eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca ../bin
jalisciense@vbox:~/Downloads/EIG-master/src>

 

[Celtion]

As you see bro, I converted them to PackedAncestryMap, I did it again, this time I downloaded and installed this Eigentools (The one you recommended me):

GitHub - DReichLab/EIG: Eigen tools by Nick Patterson and Alkes Price lab

Eigen tools by Nick Patterson and Alkes Price lab. Contribute to DReichLab/EIG development by creating an account on GitHub.

github.com

And I run it:

jalisciense@vbox:~> cd Downloads
jalisciense@vbox:~/Downloads> ls
AdmixTools EIG-master EIG-master.zip plink_linux_x86_64_20241022
jalisciense@vbox:~/Downloads> cd EIG-master
jalisciense@vbox:~/Downloads/EIG-master> cd src
jalisciense@vbox:~/Downloads/EIG-master/src> make
cc -I../include -I/usr/include/openblas -c -o baseprog.o baseprog.c
cc -I../include -I/usr/include/openblas -c -o mcio.o mcio.c
cc -I../include -I/usr/include/openblas -c -o egsubs.o egsubs.c
cc -I../include -I/usr/include/openblas -c -o admutils.o admutils.c
cc -I../include -I/usr/include/openblas -c -o h2d.o h2d.c
cc -I../include -I/usr/include/openblas -c -o eigensrc/exclude.o eigensrc/exclude.c
make -C nicksrc
make[1]: Entering directory '/home/jalisciense/Downloads/EIG-master/src/nicksrc'
cc -c -O3 -g -p -Wimplicit -I../../include -c -o strsubs.o strsubs.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o sortit.o sortit.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o vsubs.o vsubs.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o statsubs.o statsubs.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o linsubs.o linsubs.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o getpars.o getpars.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o xsearch.o xsearch.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o gauss.o gauss.c
cc -c -O3 -g -p -Wimplicit -I../../include -c -o gds.o gds.c
ar -r libnick.a strsubs.o sortit.o vsubs.o statsubs.o linsubs.o getpars.o xsearch.o gauss.o gds.o
ar: creating libnick.a
ranlib libnick.a
make[1]: Leaving directory '/home/jalisciense/Downloads/EIG-master/src/nicksrc'
cc baseprog.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o baseprog
cc -I../include -I/usr/include/openblas -c -o convertf.o convertf.c
cc convertf.o mcio.o egsubs.o admutils.o h2d.o eigensrc/exclude.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o convertf
cc -I../include -I/usr/include/openblas -c -o mergeit.o mergeit.c
cc mergeit.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o mergeit
cc -I../include -I/usr/include/openblas -c -o pca.o pca.c
cc -I../include -I/usr/include/openblas -c -o eigensrc/eigsubs.o eigensrc/eigsubs.c
cc -I../include -I/usr/include/openblas -c -o eigensrc/eigx.o eigensrc/eigx.c
cc pca.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o pca
cc -I../include -I/usr/include/openblas -c -o eigensrc/pcatoy.o eigensrc/pcatoy.c
cc eigensrc/pcatoy.o eigensrc/eigsubs.o eigensrc/eigx.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o eigensrc/pcatoy
cc -I../include -I/usr/include/openblas -c -o eigensrc/smartrel.o eigensrc/smartrel.c
cc -I../include -I/usr/include/openblas -c -o twsubs.o twsubs.c
cc -I../include -I/usr/include/openblas -c -o qpsubs.o qpsubs.c
cc -I../include -I/usr/include/openblas -c -o regsubs.o regsubs.c
cc -I../include -I/usr/include/openblas -c -o eigensrc/smartsubs.o eigensrc/smartsubs.c
cc eigensrc/smartrel.o twsubs.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o eigensrc/eigsubs.o eigensrc/eigx.o eigensrc/smartsubs.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o eigensrc/smartrel
cc -I../include -I/usr/include/openblas -c -o eigensrc/smarteigenstrat.o eigensrc/smarteigenstrat.c
cc eigensrc/smarteigenstrat.o mcio.o admutils.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o eigensrc/smarteigenstrat
cc -I../include -I/usr/include/openblas -c -o eigensrc/twstats.o eigensrc/twstats.c
cc eigensrc/twstats.o nicksrc/libnick.a -lgsl -lopenblas -lm -lpthread -o eigensrc/twstats
cc -I../include -I/usr/include/openblas eigensrc/eigenstrat.c -lgsl -lopenblas -lm -lpthread -o eigensrc/eigenstrat
cc -I../include -I/usr/include/openblas eigensrc/eigenstratQTL.c -lgsl -lopenblas -lm -lpthread -o eigensrc/eigenstratQTL
cc -I../include -I/usr/include/openblas -c -o eigensrc/smartpca.o eigensrc/smartpca.c
cc -I../include -I/usr/include/openblas -c -o gval.o gval.c
cc -I../include -I/usr/include/openblas -c -o ksrc/kjg_fpca.o ksrc/kjg_fpca.c
cc -I../include -I/usr/include/openblas -c -o ksrc/kjg_gsl.o ksrc/kjg_gsl.c
cc eigensrc/smartpca.o eigensrc/eigsubs.o eigensrc/exclude.o eigensrc/smartsubs.o eigensrc/eigx.o mcio.o qpsubs.o admutils.o egsubs.o regsubs.o gval.o nicksrc/libnick.a ksrc/kjg_fpca.o ksrc/kjg_gsl.o -lgsl -lopenblas -lm -lpthread -o eigensrc/smartpca
jalisciense@vbox:~/Downloads/EIG-master/src> make install
mv baseprog convertf mergeit pca eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca ../bin
jalisciense@vbox:~/Downloads/EIG-master/src>/CODE]

Yes, I could see that you merged in PackedAncestryMap format – that’s why I thought it was quite unusual that you had the funny alleles as I’ve only ever seen that happen with Plink files.

This is version 8 of Eigensoft you have just installed?

 

[Jalisciense]

Yes, I could see that you merged in PackedAncestryMap format – that’s why I thought it was quite unusual that you had the funny alleles as I’ve only ever seen that happen with Plink files.

This is version 8 of Eigensoft you have just installed?

it was that package ^

Or did I install it wrong?



Then I copied the executables in EIG-master bin folder to the bin folder:

Then I convert mydata plink files to PACKEDANCESTRYMAP:

jalisciense@vbox:~> cd bin
jalisciense@vbox:~/bin> convertf -p par.PACKEDPED.PACKEDANCESTRYMAP
parameter file: par.PACKEDPED.PACKEDANCESTRYMAP
genotypename: mydata.bed
snpname: mydata.bim
indivname: mydata.fam
outputformat: PACKEDANCESTRYMAP
genotypeoutname: mydata.packedancestrymapgeno
snpoutname: mydata.snp
indivoutname: mydata.ind
familynames: NO
## convertf version: 5000
genetic distance set from physical distance
ID001 ignored
all individuals set ignore.  Likely input problem (col 6)
resetting all individual...
genotype file processed
numvalidind:      1  maxmiss:  1001
packedancestrymap output
##end of convertf run
jalisciense@vbox:~/bin>

So I tried to merged them:

jalisciense@vbox:~> cd bin
jalisciense@vbox:~/bin> mergeit -p merge_param.par
parameter file: merge_param.par
geno1: v62.0_1240k_public.geno
snp1: v62.0_1240k_public.snp
ind1: v62.0_1240k_public.ind
geno2: mydata.packedancestrymapgeno
snp2: mydata.snp
ind2: mydata.ind
genooutfilename: mydata_merged_with_1240k.geno
snpoutfilename: mydata_merged_with_1240k.snp
indoutfilename: mydata_merged_with_1240k.ind
allele funny: rs2679218 T C X X
allele funny: rs7418365 A G X X
allele funny: rs2495090 C T X X
allele funny: rs6686602 G T X X
allele funny: rs97922 T G X X
allele funny: rs9645433 A G X X
allele funny: rs6678619 G A X X
allele funny: rs2149116 G A X X
allele funny: rs12097924 G T X X
allele funny: rs12566647 G A X X
allele funny: rs1772782 A G X X

Etc etc allele funny: rs etc etc

Killed
jalisciense@vbox:~/bin>

What did I do wrong?


And answering you questions about my raw data:

AncestryDNA raw data
build 37.1
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