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Post by analyst on Mar 3, 2020 18:28:03 GMT
Hi, I am trying to run -reml in GCTA. Following are log output for the code
gcta --reml --grm q1cadd --pheno WGS.Pheno.txt --out q1caddhsq --thread-num 10
*********************************************************** Accepted options:
--reml
--grm q1cadd
--pheno WGS.Pheno.txt
--out q1caddhsq
--thread-num 10
Note: the program will be running on 10 threads.
Reading IDs of the GRM from [q1cadd.grm.id].
4789 IDs read from [q1cadd.grm.id].
Reading the GRM from [q1cadd.grm.bin].
GRM for 4789 individuals are included from [q1cadd.grm.bin].
Reading phenotypes from [WGS.Pheno.txt].
Non-missing phenotypes of 4002 individuals are included from [WGS.Pheno.txt].
Assuming a disease phenotype for a case-control study: 8 cases and 1 controls
Note: you can specify the disease prevalence by the option --prevalence so that GCTA can transform the variance explained to the underlying liability scale.
9 individuals are in common in these files.
Performing REML analysis ... (Note: may take hours depending on sample size).
Error: sample size is too small.
An error occurs, please check the options or data
***********************************************************
My phenotype file has 1403 control 2599 cases, but program read this as 8 cases and 1 controls . I am not sure why is that, I really appreciate your help in debugging this error.
Thanks,
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