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jianyangqt / gcta

GCTA software
GNU General Public License v3.0
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--mpheno flag not working in gcta v1.94.1 #88

Closed RPorneso closed 4 months ago

RPorneso commented 4 months ago

I get this error when I tried using the --mpheno flag. I tried different iterations to make sure I just wasn't committing a syntax error. The following versions result in similar errors shown in the below screenshot.

--mpheno 3 pheno.txt without the --reml-pred-rand flag --mpheno pheno.txt 3 with and without the --reml-pred-rand flag (results in "invalid option 3")

image

I have ended up running the below 3 times creating 3 different files for my 3 phenotypes (these are the same outcome variables but taken from different time points). I am using GCTA to get the GBLUP as a first step before running a full mean and variance GWAS on the residualized phenotype controlling for non independence.

I am running this bash script in a Linux HPC. Thanks in advance for your attention.

longmanz commented 4 months ago

Hi, The --mpheno only works when you provide a --pheno flag. So the correct syntax would be: ./gcta ... --pheno pheno.txt --mpheno 3 .... Please re-open the issue if the issue persists and we will look into this further.