ill-conditioned #17
Description
Hello, I encountered an error when running permGWAS. The running script is as follows:
python3 ../../../../../permGWAS/permGWAS.py
-x ./allPanGenie.snpsv.h5
-y ./y_matrix.csv
-cov ./cov_matrix_comma.csv
-cov_list sex pc1 pc2 pc3 pc4
-mplot -qqplot -disable_gpu -perm 1000
The error message is as follows:
GPU is not available. Perform computations on device cpu
Working on phenotype phenotype_value
Checked if all specified files exist.
Start loading data now
Loaded data, elapsed time: 19.533646 s.
Start performing GWAS on phenotype phenotype_value for 190 samples and 8326848 SNPs.
Failure when running permGWAS2.0
linalg.eigh: (Batch element 0): The algorithm failed to converge because the input matrix is ill-conditioned or has too many repeated eigenvalues (error code: 2).
Could you please help me resolve this error? I would appreciate your assistance.