Hello everyone,

I am trying to run a meQTL analysis with tensorQTL. I prepared all necessary input files, but when I run tensorqtl.cis.map_cis( genotype_df, phenotype_df, phenotype_pos_df, covariates_df, variant_df )

I get the following AssertionError:

AssertionError Traceback (most recent call last) Cell In[103], line 2 1 #Testrun tensorQTL ----> 2 tensorqtl.cis.map_cis( 3 genotype_df, 4 phenotype_df, 5 phenotype_pos_df, 6 covariates_df, 7 variant_df 8 )

File ~/.conda/envs/mqtl_env/lib/python3.11/site-packages/tensorqtl/cis.py:645, in map_cis(genotype_df, variant_df, phenotype_df, phenotype_pos_df, covariates_df, group_s, paired_covariate_df, maf_threshold, beta_approx, nperm, window, random_tiebreak, logger, seed, logp, verbose, warn_monomorphic) 643 group_dict = group_s.to_dict() 644 if covariates_df is not None: --> 645 assert covariates_df.index.equals(phenotype_df.columns), 'Sample names in phenotype matrix columns and covariate matrix rows do not match!' 646 assert ~(covariates_df.isnull().any().any()), f'Missing or null values in covariates matrix, in columns {",".join(covariates_df.columns[covariates_df.isnull().any(axis=0)].astype(str))}' 647 logger.write(f' * {covariates_df.shape[1]} covariates')

AssertionError: Sample names in phenotype matrix columns and covariate matrix rows do not match!

However, I know that both are in the right order and have matching names and when I do covariates_df.index.equals(phenotype_df.columns) it gives out TRUE.

I am confused why this happens and wanted to reach out to hear, if anybody had same difficulties or knows how to solve this error.

Best regards