i solved the problem  replacing / with comma (5000,50000) in  naming the parameter set

Arun, have you tried to post your question to the "structure forum"? (https://groups.google.com/forum/#!forum/structure-software)

Ya I had tried but till date I am unable to get any answer of my question

Before running any program, you should understang how it works ... Do that program, have examples, so that you can be trained on how it works ... What is Ln --- in your explanation? is that a Log? .... If that is a log? ... the log of CERO does not exist ... so what you need is to know how your program works.

Try using version 2.3.2. I run 2.3.4 with windows xp. Make sure tour text file saved as Text (MS-DOS) if you are on a PC. Plody of data should be 1, any missing data should be in your file as -9 (missing dat not zeros as zeros are data, -9 signifies a lack of information) Also, do some test runs using 5000 (length of burnin) and 5000 (MCMC reps) with 3 iterations until you ger your results file to show. Then once you have the program working you should do 50000-50000 with K=1 to K=n+2 (n= number of populations) with at least 10 iterations. I hope you get it working. Structure is weird sometimes if you don't have your file in the correct format and some versions don't work well with certain operating systems.

Hi Anna, Thanks a lot. First I will try all your suggestions and then get back to you. thanks a lot

Hi Anna, I am unable to download Structure version 2.3.2 can you please provide it

Dear Sir thanks yes I have tried 2.3.4 version of the structure. But in result file I have obtained empty files with tis version

I have exactly the same problem. I´m using Structure versión 2.3.4.

Arun, did you resolve the problem?

Dear Miss Karla,

Thanks for the Response. I have tried  with Structure versión 2.3.4. but till date I am unable to resolve the problem. Do have any other idea about this.  

Hi Arun,

You may want to test a run with a very reduced sample of your datafile (I mean 10 individuals for example) and pay attention to extraspaces/returns that may cause the software to fail. It is as Structure cannot read correctly your data. Have you any extracolumns, name of markers, name of genotype ect and did you well declare all these elements?

Hi Philippe,

Thanks for the response I will first of all try with this set of data and let you know further. thanks for the response

Hi Arun,

I'm using STRUCTURE 2.3.4 and sometimes i faced the same problem as well. You need a few trial and error thou.

Hi Hong,

Thanks for suggestion. I am still trying .

i solved the problem  replacing / with comma (5000,50000) in  naming the parameter set

Dear

Gabriele Senczuk Thanks for the mail. I will try and then let you know

http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.2/html/structure.html

This seems to be a bug in the program. I'm only getting this when I try to run the program on older Macintosh computers, not on PCs (haven't tried out Linux). It doesn't seem to matter which version is used (I tried the two most recent ones) or what settings are specified.

I have had the same problem using Structure 2.3.4, with no Results files being printed. As Gabriele said, removing '"/" from the parameter name solved the problem for me. Thanks, Gabriele, nothing else I tried worked!

I have the exact same problem. Arun did you manage to find out what the problem is?? No one has solved this issue on my side yet....

Jose Javier- Try version 2.3.2. Structure is picky about inputs and such. Are you getting empty results files? You may have to rerun it. I always run some quick and dirty runs just to make sure it likes the input files and results are being generated and saved. To do this set K=3 and do your burnin/reps at a low number like 5000 and 5000. The results from these short runs ARE NOT ACCURATE, but they will give you an idea as to weather the program is running correctly. Different computers like different versions, so it may be as simple as using a different version. Or you may have something wrong with your input file. Also, make sure you are not using any forward slashes (/) in any of your file names.

The reason why the result file remains empty is that the Structure doesn't get permission to access your disk where the result file should be created. You can in a very simple way select a different directory in your computer (on other physical disk, e.g. D: or E: etc.) when you create a new project. This is the only way to get rid of the problem.The problem doesn't have anything to do with a bug in the software. It is only the lack of administrative access to the disk on your computer where the result file should be created. 

Right click on the program icon => run as administrator. This should be an alternative to changing the program directory.

Best wishes

I see this thread is old, but others may come here recently as I did.  I had the same problem using an older Mac.  I tried on my PC laptop and on a newer Mac and was able to get it to work on both of them.  Perhaps try changing the computer you are using if that is an option.

Hi, I solved the problem by running windows 7

Hi, just to add to the pool of knowledge in this threat. We had exactly the same problem and solved it with Gabrielle and Ericas suggestion of replacing the "/" with a "," (even though the / worked previously in the same structure version on the same laptop). Cheers, a

Thanks Gabriele Senczuk. My analysis worked after replacing / with ,

I have a new problem: When I run 15 iterations/replicates for every value of K, results from all the 15 runs are not getting saved in the results directory. For some values of K, I get all 15 result files, but for some just 10 or 12. This is becoming a problem when I want to compare same number of runs across different Ks to get the Evanno's delta K values. It would be great if someone could suggest a solution.

Thanks!

Ashwini

Hi all,

Does anybody faced this same problem using linux?

The front end version of the software open properly after installing. However, when all parameters are set I push RUN and nothing happens.

Thanks in advance...

No, I was trying on a Windows system. May be I will try Linux to see if the problem occurs.

Hi, Prof. Fabio Barros Britto !

How are you?

What are the Structure FE version and operating system that you are using?

In Unix systems, sometimes you need to set the permission to a folder to have the results written in that folder.

[I deleted part of this content (written in May 8th, 2019) to make it more detailed in the text below]

If you get any problems, let us know or contact me by email.

Best wishes,

João Paulo

Dear Joao, so I install java

****

openjdk version "11.0.3" 2019-04-16

OpenJDK Runtime Environment (build 11.0.3+7-Ubuntu-1ubuntu218.04.1)

OpenJDK 64-Bit Server VM (build 11.0.3+7-Ubuntu-1ubuntu218.04.1, mixed mode, sharing)

****

and run structure by both paths and whet I open project and run calculations I cannt see in black terminal in program anything and results cant save to HDD. What is it in this way& Whts is the problem?

Dear Aleksandr Kalashnikov ,

The problem is related to "read/write permissions" in the Project Folder, and Structure binary.

What OS are you using? Let’s suppose you are using a Debian based distribution (Ubuntu, Mint, Debian, etc.).

If it is about "read/write permissions", the solution is more straightforward, and we can forget all steps that I said after this statement: "In Unix systems, sometimes you need to set the permission to a folder to have the results written in that folder". (I deleted them to make these steps more simple).

The following 3 steps will work (step II and II are the most important):

Step I - Preparing the structure installation files:

1) Download a fresh copy of Structure frontend version for Linux (skip this step if you have it already).

2) Extract the tar file: tar -vzxf structure_linux_frontend.tar.gz

3) Go to the frontend folder: cd frontend

4) Are there 8 items inside this folder? (check it using ls -l)

5) Reserve this folder for later (sounds like a meal recipe hahaha).

* You will be able to see the "owner" and permissions of each item inside the folder using (ls -l).

** Do not use “sudo” or “root privileges” for any of those sub-steps (above).

Step II - Using the Java from Oracle instead of OpenJDK versions:

1) Download the Oracle Java: Click on Download Java on www.java.com website. The version used can be Linux x64.

* Despite I strongly recommend OpenJDK, it seems the Structure works better using Java from Oracle.

** No worries, you do not need to remove your preferred Java from your system. That means the following steps will be more simple.

2) Extract the JRE tar: tar -vzxf name_of_oracle_java.tar.gz (the current name is “jre-8u211-linux-x64.tar.gz”).

3 ) Reserve it for later.

Step III - “Compiling” the Structure

1) Using a system user with NO “root privileges” (a common user), go to the frontend folder (that one we reserved in Step I).

2) This is the MOST IMPORTANT SUB-STEP: Edit the Perl script “install” in the front end folder.

2.1) Find the variable $install_path=“/usr/bin/Structure” (I checked here, and it is located close to line 49 in the file)

2.2) Replace the previous path (/usr/bin/Structure) for a new path in your home directory (something like /home/my_name_here/my_structure/).

3) Run the command ./install (if you are in the frontend folder)

4) If the installer asks for a JAVA JRE, type the full absolute path to Oracle Java Binary (reserved in Step II) without spaces or special characters (Check this EXAMPLE: /home/my_name_here/Downloads/jre1.8.0_211/bin/java)

5) Press return to complete the process; you might see the message “structure v2.3.3 is installed successfully.”

6) Warning!!! The real binary will be generated in the “frontend” folder, not in the folder stated in Step III, sub-step 2.2.

7) In the frontend folder (that one used in Step I), you will find a new structure binary, close to the pearl script “install” that we edited before.

8) Using the command-line, type ./structure, and you will be able to run the structure and get the result files for sure.

Final considerations:

- If your default Java is an Oracle Java (or if it is well set), the installer script will not ask for JAVA JRE in Step III, sub-step 4.

- You do not need any user privileges. Also, it is better if you perform all those steps using a “common user” without privileges (no sudo or root).

- Type ls -l in the folder… you will be able to see your brand-new binary assigned to your “common-user” with no root privileges.

- To make sure everything will work, check if you have full Read/Write in your Project Folder.

Sorry for this long text, and the grammar-spelling mistakes.

Let me know if those instructions worked for you.

Cheers,

João

Dear João Paulo Gomes Viana ,

Thanks very much for your tutorial for installing and running Structure in Debian. After editing the install script it runs as expected.

Abraços,

Pedro

Dear Pedro Poli ,

I am happy to hear that.

Best wishes,

João

probably, I solve that with reinstall java and place of work folder in system. Thanks!

Hello João Paulo Gomes Viana,

How is it going so far?

We are good here! I hope you're well too.

Thanks for your reply... I'll try to find out whats going on following your recommendation.

Cheers,

Fábio