Question: Admixture give me an error with ped "PLINK Input file error" and with bed format quit with error message "Abort trap6
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gravatar for rajneeshpaliwal
3.1 years ago by
rajneeshpaliwal0 wrote:

Dear all biostar users, 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

software error • 1.8k views
ADD COMMENTlink modified 12 days ago by daniele.buo0 • written 3.1 years ago by rajneeshpaliwal0

Hi, I got the same error with ped file. Did you find a solution? :)

ADD REPLYlink modified 12 days ago • written 12 days ago by daniele.buo0

The OP of this question did not log in for years. I suggest you post a new question, add the necessary code and details and highlight code/data examples with the format bar (10101) to make it visually-appealing (this post here is clearly not). You might then get a response from the PLINK folks. Also be sure to add PLINK as tag instead of something like software error as OP did above.

ADD REPLYlink modified 12 days ago • written 12 days ago by ATpoint24k
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