ADMIXTURE

[chris blair]

I am learning to run ADMIXTURE for the first time and am receiving a PLINK input file error. I used VCFtools to convert a vcf file to PLINK (./vcftools --vcf filename --plink --thin 150 --out filename). 

I am running ADMIXTURE using the following command:

./admixture filename.ped 3

Any help would be appreciated.

Chris

[Vikram Chhatre]

Exclude the ".ped" extension.  It's assumed.  Make sure there are three files with the same prefix in that folder.

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[chris blair]

Hey Vikram, 

If I do that I receive a message stating that the input data file argument must have an extension.

Chris

On Friday, 17 March 2017 16:29:33 UTC-4, Vikram Chhatre wrote:

Exclude the ".ped" extension.  It's assumed.  Make sure there are three files with the same prefix in that folder.

On Fri, Mar 17, 2017 at 2:17 PM, chris blair <blai...@gmail.com> wrote:

I am learning to run ADMIXTURE for the first time and am receiving a PLINK input file error. I used VCFtools to convert a vcf file to PLINK (./vcftools --vcf filename --plink --thin 150 --out filename). 

I am running ADMIXTURE using the following command:

./admixture filename.ped 3

Any help would be appreciated.

Chris

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[chris blair]

I guess it wasn't in the correct .ped format...

[Vikram Chhatre]

Yes, I was looking at my files and it took me down the rabbit hole.  You just need one more step:

plink --noweb --file input_prefix --recode12 --out output_prefix

Then use the same command for admixture as you did first.

On Fri, Mar 17, 2017 at 2:44 PM, chris blair <blai...@gmail.com> wrote:

I guess it wasn't in the correct .ped format...

On Friday, 17 March 2017 16:33:50 UTC-4, chris blair wrote:

Hey Vikram, 

If I do that I receive a message stating that the input data file argument must have an extension.

Chris

On Friday, 17 March 2017 16:29:33 UTC-4, Vikram Chhatre wrote:

Exclude the ".ped" extension.  It's assumed.  Make sure there are three files with the same prefix in that folder.

On Fri, Mar 17, 2017 at 2:17 PM, chris blair <blai...@gmail.com> wrote:

I am learning to run ADMIXTURE for the first time and am receiving a PLINK input file error. I used VCFtools to convert a vcf file to PLINK (./vcftools --vcf filename --plink --thin 150 --out filename). 

I am running ADMIXTURE using the following command:

./admixture filename.ped 3

Any help would be appreciated.

Chris

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[chris blair]

Hi Vikram, 

Sorry I have another question. I am running ADMIXTURE using the script provided in the manual to determine the appropriate K (1-10). When the analysis reaches K = 6 I am getting nan for LogLikelihood and delta. Any idea what this means?

Chris

On Friday, 17 March 2017 16:46:17 UTC-4, Vikram Chhatre wrote:

Yes, I was looking at my files and it took me down the rabbit hole.  You just need one more step:

plink --noweb --file input_prefix --recode12 --out output_prefix

Then use the same command for admixture as you did first.

On Fri, Mar 17, 2017 at 2:44 PM, chris blair <blai...@gmail.com> wrote:

I guess it wasn't in the correct .ped format...

On Friday, 17 March 2017 16:33:50 UTC-4, chris blair wrote:

Hey Vikram, 

If I do that I receive a message stating that the input data file argument must have an extension.

Chris

On Friday, 17 March 2017 16:29:33 UTC-4, Vikram Chhatre wrote:

Exclude the ".ped" extension.  It's assumed.  Make sure there are three files with the same prefix in that folder.

On Fri, Mar 17, 2017 at 2:17 PM, chris blair <blai...@gmail.com> wrote:

I am learning to run ADMIXTURE for the first time and am receiving a PLINK input file error. I used VCFtools to convert a vcf file to PLINK (./vcftools --vcf filename --plink --thin 150 --out filename). 

I am running ADMIXTURE using the following command:

./admixture filename.ped 3

Any help would be appreciated.

Chris

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[chris blair]

Interestingly, I do not get this error when I run K=7. This is quite strange. I googled this issue and apparently others have run into similar problems. Do you have any recommendations? Can I simply not test K=6? This seems odd.

Chris

[Ana Beatriz Bueno]

Hi, everyone!

I'm trying to run ADMIXTURE, but I only have .geno format file and it shows a message that this format is no long supported, Any of you know which software/converter I could use to change from .geno to .ped??

Thanks a lot!!!
Ana