Error message when trying to use STRUCTURE analysis

[Rafa Martin]

Hi, noob user here.

I was trying to perform a STRUCTURE analysis on my dataset from dartseq (SL8, which is a large dartR object containing the filtered info on SNP and pop info files provided by the seq services) using the "gl.run.structure".

I keep getting the message that I have not installed STRUCTURE software (though i have it already installed). What I am getting wrong? (maybe I'm not writing the path correctly?)

Thanks a lot for the help!

My STRUCTURE software path is this: 

C:\Program Files (x86)\Structure2.3.4

My code so far is this: 

STR <- gl.run.structure (SL8, exec = "C:/Program Files (x86)/Structure2.3.4") Starting gl.run.structure Processing genlight object with SNP data Error in FUN(X[[i]], ...) : You do not have STRUCTURE installed.

[Jose Luis Mijangos]

Hi,

Can you try the following solutions:

1. Move the executable file (it has a ".exe" extension in a PC) to a directory without spaces. 

2. Find the path of the executable. Here are some ways to find it:  https://www.wikihow.com/Find-a-File%27s-Path-on-Windows 

3. Copy and paste the path into the function and then run again the function. 

Cheers,

Luis

[Bernd.Gruber]

Also there might be a problem that you have a “space” in your path and if I am not mistaken

 

Structure does not like that when creating its temporary folder, though it might be okay with the exec argument.

 

Cheers, Bernd

 

 

 

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From: da...@googlegroups.com <da...@googlegroups.com> On Behalf Of Jose Luis Mijangos
Sent: Tuesday, 18 April 2023 08:28
To: dartR <da...@googlegroups.com>
Subject: [dartR] Re: Error message when trying to use STRUCTURE analysis

 

Hi,

 

Can you try the following solutions:

 

1. Move the executable file (it has a ".exe" extension in a PC) to a directory without spaces. 

2. Find the path of the executable. Here are some ways to find it: https://www.wikihow.com/Find-a-File7s-Path-on-Windows

3. Copy and paste the path into the function and then run again the function. 

 

Cheers,

Luis

On Tuesday, 18 April 2023 at 6:02:28 am UTC+10 ginko...@gmail.com wrote:

Hi, noob user here.

I was trying to perform a STRUCTURE analysis on my dataset from dartseq (SL8, which is a large dartR object containing the filtered info on SNP and pop info files provided by the seq services) using the "gl.run.structure".

I keep getting the message that I have not installed STRUCTURE software (though i have it already installed). What I am getting wrong? (maybe I'm not writing the path correctly?)

Thanks a lot for the help!

 

My STRUCTURE software path is this: 

 

C:\Program Files (x86)\Structure2.3.4

 

My code so far is this: 

 

STR <- gl.run.structure (SL8, exec = "C:/Program Files (x86)/Structure2.3.4") Starting gl.run.structure Processing genlight object with SNP data Error in FUN(X[[i]], ...) : You do not have STRUCTURE installed.

 

 

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[Rafa Martin]

Thanks for the answers!, It seems that moving it to a location without spaces worked =). 

Nonetheless I have another doubt regarding the STRUCTURE analyses with the package. 

After running the "gl.run.structure" function I wanted to use the plot an map ones, but it is giving me problems. As far as I'm concerned, I have to use the run object and the  Q-matrix from the analisis to run the plot and map functions but I'm not doing it well. Do I need to extract those from the analysis with aditional steps or can I use the STR itself further on?

Also, I don't have very clear what is actually the the lat/long object for the map function. I have a txt file with the lat/long info for my sites apart from my metadata file for the dart with the SNP's, is that any of those?? My code would be something like this:

# Run STRUCTURE analysis
STR <- gl.run.structure (SL8, exec = "C:/strucutre/structure_windows_console/console/structure.exe", k.range = 1:4, num.k.rep = 10, noadmix = FALSE)

# Generate plots with gl.plot.structure(), specifying Q-matrix as input
STRplot <- gl.plot.structure(STR, K=4)


STRmap <- gl.map.structure(STRplot, latlong.txt, K=4)

Thanks again for the help!!!