Maximum number of Markers?

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Karl Effertz

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Nov 28, 2022, 4:47:34 PM11/28/22
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Hello, 

I am attempting to run Structure (GUI - version 2.3.4) on a dataset containing 314 diploid individuals with 50,842 markers. When input the data file for the new project it just gives me a black screen in the top right and bottom panels of the user interface. No error messages or anything, just a black box. 

I had just run a practice round with a dataset of ~300 diploid individuals and ~550 markers and that project is working just fine. 

Does structure have a maximum number of markers? Will I need to trim my data down in order to run Structure? 

Thanks, 

Karl 

Josh Banta

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Nov 29, 2022, 10:11:18 AM11/29/22
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Dear Karl,

As far as I know, STRUCTURE cannot be multi-threaded, so it does bottleneck like this.

I suspect you are using some sort of reduced representation sequencing approach like RAD-seq. Or perhaps you have whole-genome data and you picked out the SNPs bioinformatically.

I have done analyses like this using STRUCTURE, although with closer to 20 individuals rather than 300. I think I had something like 50,000 SNPs as well. As I recall it took weeks to run but it did get there. I'm not sure how much faster it would run on a better computer, although I presume having a lot of RAM would help prevent RAM-limiting problems. But the number cores wouldn't matter I don't think.

One thing you could do for RAD-seq data is thin your SNPs down to one SNP per RAD-seq fragment. This is probably a good thing anyway, so that your markers are more unlinked and more independent of one another. I tried this, and it reduced the number of markers from 50,000 down to something like 300 or 1,000. I found that STRUCTURE still took a very long time to run, but I would have to expect it reduces the run time.

I hope this helps.

Best,
Josh

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Josh Banta

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Nov 29, 2022, 10:14:56 AM11/29/22
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PS: I would be re-miss if I did not suggest FASTStructure, but I personally do not trust it. You can see my thoughts about it here:

On Nov 28, 2022, at 3:46 PM, Karl Effertz <karle...@gmail.com> wrote:

Francisco Pina Martins

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Nov 30, 2022, 3:49:35 AM11/30/22
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Dear Karl,

Building on Josh's answer, allow me to add that if you are willing to use a command line version of STRUCTURE, there is software that is able to parallelize it, with a linear increase in speed per core used.

Best,

Francisco

Emmanuel AMPONSAH ADJEI

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Dec 4, 2022, 9:08:17 AM12/4/22
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Dear Karl, 

I have been having similar issues. Since the markers are large, it will take time before they load into the system. 

You have to keep trying until it loads for you. Other than that, I don't know any solution. 

Best of luck.


Amponsah

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Josh Banta

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Dec 4, 2022, 2:44:24 PM12/4/22
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Yes, I forgot about those! If you want to get comfortable with command-line STRUCTURE, you can watch my tutorial here:


From there you should be able to adapt it to work with STRUCTURE threader to use multiple cores.

Best,
Josh

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