2022-02-16 11:25:58,701 glint INFO      methylation_data.py:156        Loading file datafile.txt...
2022-02-16 11:25:59,769 glint INFO      methylation_data.py:680        Checking for missing values in the data file...
2022-02-16 11:25:59,778 glint INFO      methylation_data.py:227        Validating covariates file...
2022-02-16 11:25:59,778 glint INFO      methylation_data.py:156        Loading file covariates.txt...
2022-02-16 11:25:59,783 glint INFO      methylation_data.py:229        New covariates were found: age, gender, chip1, chip2, chip3, chip4, chip5, chip6, chip7, chip8.
2022-02-16 11:25:59,867 glint INFO      epistructure.py:19             Running EPISTRUCTURE...
2022-02-16 11:25:59,867 glint INFO      epistructure.py:20             Removing non-informative sites...
2022-02-16 11:25:59,867 glint INFO      methylation_data.py:368        Including sites...
2022-02-16 11:26:03,237 glint INFO      methylation_data.py:371        Include sites: 534 CpGs from the reference list of 4913 CpGs will be included...
2022-02-16 11:26:03,262 glint INFO      methylation_data.py:326        49466 sites out of 50000 were excluded (534 sites left).
2022-02-16 11:26:03,262 glint INFO      methylation_data.py:622        Using covariates age, gender.
2022-02-16 11:26:03,262 glint INFO      epistructure.py:25             Regressing out covariates...
2022-02-16 11:26:03,419 glint INFO      epistructure.py:30             Running PCA...
2022-02-16 11:26:03,428 glint INFO      epistructure.py:39             The first 1 PCs were saved to glint_results_tutorialdata.epistructure.pcs.txt.
2022-02-16 11:26:03,429 glint INFO      methylation_data.py:306        Added covariates epi1.
