Comments (5)
I am also hitting this error. Did you solve it in the end?
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Have you masked the individuals who you want to predict the phenotypes for? To do that, you can replace their phenotype values in the phenotype file with NA.
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Just thought I'd post to say that solved the problem. Thanks for the quick response!
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@xiangzhou I'm labeling this as a bug because it would be helpful to have proper error handling---and give a more informative error message---before a segmentation fault is reached.
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I am closing this issue. Yes, we should have proper error handling. But it is a largish subject. Best to keep adding enforce_msg statements etc.
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Related Issues (20)
- Issue with GEMMA-Wrapper HOT 1
- Parsing input file '' failed in function AnalyzeBimbamGXE
- Enforce failed for number of analyzed individuals equals 0. in src/param.cpp at line 2073 in ProcessCvtPhen HOT 2
- long haplotype as population structure
- basic usage doesn't work
- Gemma run-time for Estimate Relatedness Matrix calculation
- very low number of analyzed SNPs/var
- The input files includes 26 linkage groups but the output files only includes 22 linkage group
- Categorical covariates
- Pve is .999 HOT 1
- gemma-wrapper:279:in `<main>': Expected GEMMA -a genotype file switch (RuntimeError)
- Got a nan in the p-value results HOT 1
- gsl: newton.c:88: ERROR: function value is not finite 3.08%
- GSL ERROR: function value is not finite in brent.c at line 58 errno 9
- WARNING: Brent did not converge
- Why the diagonal of relatedness matrix is not equal to 1 or a constant value? HOT 1
- The problem of filtering snp parameters
- ERROR: Enforce failed for Problem reading FAM file (phenotypes do not match geno file) in src/gemma_io.cpp at line 600 in ReadFile_fam GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
- Identical P-Values at end of run HOT 1
- BIMBAM format (preferred)
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