PLINK file from populations

Vincent Biard

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Oct 16, 2015, 6:24:03 AM10/16/15

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Hi

I have a little problem using the population pipeline. I have ask a PLINK file so I can use that in ADMIXTURE, however Admixture give me an error "PLINK Input file error"…

Does anyone experience this before?? Does anyone know if the .ped file 12 coded?

Thanks for your help

Vincent

Flavia Termignoni

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Oct 16, 2015, 12:34:58 PM10/16/15

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For me .ped files have been working fine for a lot of things on PLINK and other programs.

Have you tried to eliminate the first line (#stacks info) to check if that could be the problem?

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Meghana Natesh

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Oct 18, 2015, 1:24:19 AM10/18/15

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Hi,

I have a similar problem with the plink files in admixture. I get the same error and have not been able to figure it out. If someone has any suggestions, it would be great.

Thanks,
Meghana

Matthew Combs

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Oct 18, 2015, 11:27:05 AM10/18/15

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I have been able to use Admixture after converting the plink files to a .bed format.

Use the "--make-bed" command in plink.

Good luck,
Matt

Li

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Feb 7, 2016, 10:05:49 AM2/7/16

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Hi Matt and Vincent

Matt, can you please explain a little bit more about the " --make-bed" in plink, I tried to do it on the .ped file with no sucsses. and even if for the admixture when I use bed i need also .bim and .fam how do you create those and from what file?

Vincent, have you menage to solve this problem in a different way?

thanks

L

Rajneesh Paliwal

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Sep 7, 2016, 6:00:09 AM9/7/16

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Dear Meghana,

I have a problem in use of both ped and bed feel in admixture software. Admixture give me an error with ped "PLINK Input file error" and with bed format quit with error message "Abort trap: 6".
Here I am using scaffolds number in place chromosome number and Fingermillet is non-reference genome crop.

Is any one who can do my urgent help

Error message with ped

hotspot:admixture_macosx1.3 Rpaliwal$ ./admixture ../Plink_File_FM_peter/FMillet_11KSNP.plk.ped 2 -j4

**** ADMIXTURE Version 1.3.0 ****

**** Copyright 2008-2015 ****

**** David Alexander, Suyash Shringarpure, ****

**** John Novembre, Ken Lange ****

**** ****

**** Please cite our paper! ****

**** Information at www.genetics.ucla.edu/software/admixture ****

Parallel execution requested. Will use 4 threads.

Random seed: 43

Point estimation method: Block relaxation algorithm

Convergence acceleration algorithm: QuasiNewton, 3 secant conditions

Point estimation will terminate when objective function delta < 0.0001

Estimation of standard errors disabled; will compute point estimates only.

PLINK Input file error

Error message with bed

hotspot:admixture_macosx1.3 Rpaliwal$ ./admixture ../Plink_File_FM_peter/plink.bed 2 -j4

**** ADMIXTURE Version 1.3.0 ****

**** Copyright 2008-2015 ****

**** David Alexander, Suyash Shringarpure, ****

**** John Novembre, Ken Lange ****

**** ****

**** Please cite our paper! ****

**** Information at www.genetics.ucla.edu/software/admixture ****

Parallel execution requested. Will use 4 threads.

Random seed: 43

Point estimation method: Block relaxation algorithm

Convergence acceleration algorithm: QuasiNewton, 3 secant conditions

Point estimation will terminate when objective function delta < 0.0001

Estimation of standard errors disabled; will compute point estimates only.

Abort trap: 6

Thanks in advance for kind help

Regards

Rajneesh

Admixture_Errormessage_with_ped&bed.docx

Nicolas Rochette

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Sep 12, 2016, 11:02:12 AM9/12/16

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Hi Rajneesh,

ADMIXTURE's error is quite laconic, so I can't really help. Do you have an idea of what is wrong with your PLINK files ? Do they exist (in the right place) and look correct (esp., are they not truncated) ?

Best,

Nicolas

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Lilnet Cloud

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Nov 24, 2016, 10:45:45 PM11/24/16

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Hi Rajneesh,

Hopefully you would have solved your problem by now and I am putting this out there for anyone who faced the same problem.

I managed to get admixture to run with plink files only after recoding the original binary file output from plink using:

./plink -bfile filename --recode12 -out filename2

this generates a .ped and .map file that can be used in admixture

Cheers!

Elize

Alicia Mastretta

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Aug 15, 2017, 2:14:53 PM8/15/17

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Hi,

Just to confirm that Elize's solution works and that it has nothing to do with the #first line, truncated file, etc.

Chris S

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Apr 30, 2018, 12:29:07 PM4/30/18

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I had the same error message, and I learned that for me the error was coming from absent meta-info columns in the .ped file. For example, plink and admixture apparently expect "sex" and "parents" and other columns, which I did not have. A quick fix is to convert to .bed format as Matthew posted above, including* the flags "--allow-no-sex --no-sex --no-parents --no-fid --no-pheno". Then running admixture using the .bed data.