Running STRUCTURE

[Damian Alexandridis]

Hi all, 
I'm trying to run the STRUCTURE software for the first time but i get errors including my input file.
My data is consisted from 348 individuals and 950 loci. The final2.structure file (input) has in the first column, the individuals, in the 2nd, the corresponding population each individual belongs to and then 950 columns for the loci. Also, the data is organised as two rows per individual. So 696 rows with genotype data and the first row with the marker/loci names.
The error message is in the below screenshot.  

I hope i gave you enough info about my problem.
Thank you in advance.

Damian
 

[Josh Banta]

Dear Damian,

The STRUCTURE file format is very unforgiving. Any slight deviation will cause it to fail. For instance, you may have a blank line on row 697.

I have a step-by-step tutorial for converting from FASTA to STRUCTURE file format that you may want to check out. It is written for Ubuntu Linux, but it is not required. You can use any operating system, as long as you have R and Rstudio installed.

https://youtu.be/EO6AtZPgz1g

Best wishes,

Josh

On Jul 10, 2023, at 12:54 AM, Damian Alexandridis <damianosalex...@gmail.com> wrote:

Hi all, 
I'm trying to run the STRUCTURE software for the first time but i get errors including my input file.
My data is consisted from 348 individuals and 950 loci. The final2.structure file (input) has in the first column, the individuals, in the 2nd, the corresponding population each individual belongs to and then 950 columns for the loci. Also, the data is organised as two rows per individual. So 696 rows with genotype data and the first row with the marker/loci names.
The error message is in the below screenshot.  

I hope i gave you enough info about my problem.
Thank you in advance.

Damian
 <Error in STRUCTURE.png><mainparams.png><extraparams.png><final2.stru.png>

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<mainparams.png><extraparams.png><Error in STRUCTURE.png><final2.stru.png>

[Damian Alexandridis]

Thank you Josh for the help,
I solved the problem by changing a few things :  population IDs should only be integers (i had also some strings), individuals' names were changed to numbers (this step might not be neseccery), and the most important thing was to change the file format to unix with the "dos2unix" command.  The input file was first made in windows environment and then used in unix.  I didnt take that into account.  

Cheers,

Damian

To view this discussion on the web visit https://groups.google.com/d/msgid/structure-software/397EE310-E219-4952-A92F-2197372A5B5C%40gmail.com.