Parsing input file '' failed in function AnalyzeBimbamGXE

[MaxiEstravis]

Hi all, thanks for the great work in GEMMA.
I'm trying to do an analysis with a bim genotype file, a phenotype file, and a GxE file. This is the Linux command line:

~/tools/GEMMA/bin/gemma -g test.bim -p test_pheno.txt -n 1 -a test.anno -k ./output/test_matrix.cXX.txt -gxe test_2021_bio1.data -lmm 4 -o test_BranchQuality_2021_bio1_lmm

This gives the following log with an error:

GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
Reading Files ... 
## number of total individuals = 3
## number of analyzed individuals = 3
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =  2046023
## number of analyzed SNPs         =  1177875
Start Eigen-Decomposition...
pve estimate =3.06394e-06
se(pve) =6.45794
**** FAILED: Parsing input file '' failed in function AnalyzeBimbamGXE in src/lmm.cpp at line 2329

Because of this error, I suspect that something is wrong with the GxE file, which looks like this:

3.3
4.1
2.9

According to the manual specification (Page 21):

This gxe file contains a column of environmental variables

Besides, this following line without invoking the GxE file works perfectly:

~/tools/GEMMA/bin/gemma -g test.bim -p test_pheno.txt -n 1 -a test.anno -k ./output/test_matrix.cXX.txt -lmm 4 -o test_BranchQuality_2021_bio1_lmm

I noticed there's a related issue that's planning to be incorporated in the new release (Issue #241), but does this mean that I can't incorporate GxE in my analysis for now? Or did I do something wrong?

Cheers,
Maximiliano.

[JoannaGriffiths]

Hello,
I am running into the same issue with version 0.98.3. Has this issue been resolved? Thank you!