EEMSpath

[laiaju...@gmail.com]

Hi all,

I am trying to run the EEMS analysis. However, I have been trying to run it and am having the same error with the path. I am sure the file is there, but I have the same error too many times. 

I would love it if somebody could help me, please. 

eems.path <- "C:/Users/User/Desktop/runeems_snps.exe/"
 
 eems <- gl.run.eems(gl2, buffer = 1000, eems.path =eems.path, nDemes = 50, diploid = TRUE,
                     numMCMCIter = 10000, numThinIter = 99, numBurnIter = 5000, add_demes=TRUE,
                     add_grid=TRUE, out.dir=tempdir())
 

+ add_grid=TRUE, out.dir=tempdir()) Starting gl.run.eems Cannot find runeems_snps.exe in the specified folder given by eems.path: C:/Users/User/Desktop/runeems_snps.exe/ Error in gl.run.eems(gl2, buffer = 1000, eems.path = eems.path, nDemes = 50, :

[Bernd.Gruber]

Hi,

can you try to remove the forward slash at the end in your eems.path statemeny.

Cheers, Bernd

---

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To: dartR <da...@googlegroups.com>
Subject: [dartR] EEMSpath

 

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[Laia Juliana Muñoz]

Hi Bernd,

I did that, too, but I still can not run it.

Thanks,

Laia

Starting gl.run.eems 
  Cannot find runeems_snps.exe in the specified folder given by eems.path: C:/Users/User/Desktop/runeems_snps.exe 

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[Bernd.Gruber]

Hi Laia,

First the path seems to be a bit unusual but I guess that is okay (…/users/user/ )

But looking at it it means run_eems seems to be on your desktop. So you should see it the, is that true. Can you double click on it to check that you can run it.

A terminal window should open briefly.

Also you are working on a windows machine, correct?

Cheers, Bernd

---------

On 6 May 2024, at 08:56, Laia Juliana Muñoz <laiaju...@gmail.com> wrote:



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[Laia Juliana Muñoz]

Hi Bernd,

Yes, I am using a Windows machine. 

I am using the file that you provided during the workshop. However, when I click on it the window below appears. When I copy the path it is how it looks: "C:\Users\User\Desktop\runeems_snps".

Thanks,

Laia

To view this discussion on the web visit https://groups.google.com/d/msgid/dartr/7C92ADDA-032A-488E-9FEF-01246BE26A64%40canberra.edu.au.

[Bernd.Gruber]

Okay I think I know.

Provide only the path not the exe so should read

C:\Users\User\Desktop

Only as the eems.path argument

Cheers, Bernd

---------

On 6 May 2024, at 09:11, Laia Juliana Muñoz <laiaju...@gmail.com> wrote:



Hi Bernd,

Yes, I am using a Windows machine. 

I am using the file that you provided during the workshop. However, when I click on it the window below appears. When I copy the path it is how it looks: "C:\Users\User\Desktop\runeems_snps".

Thanks,

Laia

<image.png>

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[Laia Juliana Muñoz]

Hi Bernd,

I already tried, but it did not work either. 

Best,

Laia

>  eems.path <- "C:/Users/User/Desktop"

>  eems <- gl.run.eems(gl2, buffer = 1000, eems.path =eems.path, nDemes = 50, diploid = TRUE,

+                      numMCMCIter = 10000, numThinIter = 99, numBurnIter = 5000, add_demes=TRUE,

+                      add_grid=TRUE, out.dir=tempdir())
Starting gl.run.eems 
  Cannot find runeems_snps.exe in the specified folder given by eems.path: C:/Users/User/Desktop 

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[Jose Luis Mijangos]

Hi Laia,

Try using a forward slash after the folder name that contains the executable file. 

If the executable is in the working directory, you can run it as below:

library(dartRverse)
dartRverse_install(package = "dartR.spatial", rep = "github", branch = "dev")
library(dartR.spatial)
library(sf)
t1 <- platypus.gl
t1 <- gl.filter.callrate(t1,threshold = 1)
t1$other$latlon
eems <- gl.run.eems(t1,
                    buffer = 1000,
                    eems.path ="./",

                    nDemes = 50,
                    diploid = TRUE,
                    numMCMCIter = 10000,
                    numThinIter = 99,
                    numBurnIter = 5000,
                    add_demes = TRUE,
                    add_grid = TRUE,

                    out.dir = getwd()
                    )

Cheers,

Luis 

[Laia Juliana Muñoz]

Hi Jose Luis,

I tried both using the file on the desktop and moving it to my working directory, but nothing happened. 

Best,

Laia

>  library(dartR.spatial)
**** Welcome to dartR.spatial [Version 0.89 ] ****

>  library(sf)
>  t1 <- gl2

>  t1 <- gl.filter.callrate(t1,threshold = 1)

Starting gl.filter.callrate 
  Processing genlight object with SNP data
  Recalculating Call Rate
  Removing loci based on Call Rate, threshold = 1 
Completed: gl.filter.callrate 
>  t1$other$latlon
                           lat        lon
STR-2-2015           -4.022000  -82.95300
MEX-38-2015          20.985000 -109.53900
STR-9-2016           -4.022000  -82.95300

>  eems.path <- "C:/Users/User/Desktop/"
>  eems <- gl.run.eems(t1,
+                      buffer = 1000,
+                      eems.path ="C:/Users/User/Desktop/",
+                      nDemes = 50,
+                      diploid = TRUE,
+                      numMCMCIter = 10000,
+                      numThinIter = 99,
+                      numBurnIter = 5000,
+                      add_demes = TRUE,
+                      add_grid = TRUE,
+                      out.dir = getwd()
+  )
Starting gl.run.eems 
  Cannot find runeems_snps.exe in the specified folder given by eems.path: C:/Users/User/Desktop/ 
Error in gl.run.eems(t1, buffer = 1000, eems.path = "C:/Users/User/Desktop/",  : 
  
> setwd("C:/Users/User/Desktop/Tuna research/Bases de datos/Genómica/Report-DTu24-9051")
>  eems <- gl.run.eems(t1,
+                      buffer = 1000,
+                      eems.path ="./",
+                      nDemes = 50,
+                      diploid = TRUE,
+                      numMCMCIter = 10000,
+                      numThinIter = 99,
+                      numBurnIter = 5000,
+                      add_demes = TRUE,
+                      add_grid = TRUE,
+                      out.dir = getwd()
+  )
Starting gl.run.eems 
  Cannot find runeems_snps.exe in the specified folder given byseemss.path: ./ 
Error in gl.run.eems(t1, buffer = 1000, eems.path = "./", nDemes = 50,  : 
  

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[Bernd.Gruber]

What do you see when you try

dir("C:\Users\User\Desktop")

---------

On 6 May 2024, at 11:04, Laia Juliana Muñoz <laiaju...@gmail.com> wrote:



Thanks,

Laia

<image.png>

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Sent: Sunday, 5 May 2024 6:22 AM

To: dartR <http://da...@googlegroups.com>
Subject: [dartR] EEMSpath

 

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