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Error: Not all three ind/snp/geno files present #84
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Hi, first of all, are you sure that your path to the EIGENSTRAT trio is correct? I.e. that your prefix corresponds to the correct path to the data? For instance, I see this:
So the files are in Then I can do this in R:
Based on what you wrote, my assumption is that you forgot to add the part of the path that is shared by all three files ( I don't see any problem with the files. Or at least nothing that would prevent admixr from loading them. I don't know what |
I copied the files to downloads, and used this codes. I got same error: Not all three ind/snp/geno files present. I also tried using the example data, but I got another error.
|
If the package tells you that the files are not present, this means that your path is simply not correct. This is literally what the Please do the following:
Please paste here exactly what you typed in R, including the path.
Both of these might be true. However, this has nothing to do with the error you're getting. Let's focus on solving your issue first. |
Did you have any success? One more piece of information that I can provide: in your initial message you write that you specified the prefix as
However, given the structure of the zipped EIGENSTRAT data that you provided (which has a common prefix
? This is, in fact, what I did in my reply. |
Not yet! |
Closing due to inactivity. Happy to reopen again if necessary. |
Hi Martin,
I tried running AdmixR in R after installing admixtools in R and as well as on ubuntu. I converted into eigenstrat using "vcf2eignestrat.py" I got the 3 files (.ind, .snp and .geno).
I created the .Renviron and I linked the path from my ubuntu (admixtools).
Finally, I tried loading the data using this command,
set data prefix
data_prefix <- "./MontisAdmixR"
data_prefix
read in data
snps <- eigenstrat(data_prefix)
I got this error... "Error: Not all three ind/snp/geno files present"
Kindly check out the files and probably proffer a solution.
Thank you,
Bashir
MontisAdmixR.zip
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