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genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association
https://github.com/genetics-statistics/GEMMA
GNU General Public License v3.0
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FAILED error #259

Open SNgalaxy opened 2 years ago

SNgalaxy commented 2 years ago

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  1. [X] I have found an issue with GEMMA
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SNgalaxy commented 2 years ago

Hi There,

I have searched for this error everywhere and I can't get it worked. I am trying to use the IBS matrix from plink in GEMMA and it gives me the error below:

**** FAILED: number of columns in the kinship file does not match the number of individuals for row = 0

the IBS matrix is built by the --distancs ibs flag in plink and the Gemma code is as below. I appreciate it of you could let me know what is the issues? I am trying to correct for the repeated measurements in my samples.

gemma-0.98.5-linux-static-AMD64 -bfile tmp.genotype \ -p expression.txt \ -km 1 -k IBS_matrix.mibs \ -lmm 4 -o association_outcome

Regards, SN