Running Structure from the command line

[Jermaine]

Hi All,

I am new to STRUCTURE and have just learned the basics of running it using the front end, but have discovered that my SNP data set is too large for the program to handle on my Windows machine (would take a month to complete an analysis). I would instead like to be able to initiate STRUCTURE from the command line so that I can submit a script to my university's slurm job scheduler and have the analysis run on a computing cluster, but am having a hard time figuring out how to do this via the STRUCTURE 2.3 manual.

The manual lists out and describes all of the program parameters, and how to format them for inclusion in a user-prepared .txt file called mainparams; as I understand it, STRUCTURE will read this file to know what parameters to use for the analysis. What the manual doesn't seem to explain (as far as I can tell) is how to actually invoke STRUCTURE on the command line, specifically with regard to directing the program to read a data input file and a mainparams file. Invoking STRUCTURE itself is probably something simple like just typing structure, but after that what does the rest of the command look like? I imagine maybe something like...

structure -option /path/to/directory/containing/datafile -option /path/to/directory/containing/mainparams

...but as mention, the manual doesn't seem to provide a basic example script for running the program on the command line. Can anyone show or direct me to such an example?

Additionally, on inspecting the mainparams file outputted from running the program on the front end using a small SNP data set as a test run, I noticed that the file did not contain a parameter for setting the number of iterations to run per K. On thinking about it, this made sense since on the front end interface the number of iterations was not entered while setting the analysis parameters, but instead entered on the window that pops up after hitting run project from the project drop-down menu, right before actually running the analysis. So I guess an additional question I have is how do I set the number of iterations per K through initiating the program on the command line? Again, I imagine maybe something like...

structure -option /path/to/directory/containing/datafile -option /path/to/directory/containing/mainparams -option #iterations

Apologies for the long-winded post, I just really need to get my eyes on a working example for this and wanted to be as clear as I could manage. Thank you to anyone taking the time to read this and much appreciation in advance for any assistance.

[Vikram Chhatre]

https://strauto.popgen.org

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