error with --return_dense

[liaguiro]

Hello,

I'm running the tensorqtl with the trans mode, and it works, but I get an error when I run it with --return_dense to get the beta values.

python3 -m tensorqtl SNPs.step5.v2.reconstructed TPMmatrix.tensorqtl_format.bed interaction.clones --covariates covariance.matrix.txt --interaction interaction.info.txt --mode trans -o test.trans.dense.output --window 500000 --return_dense

can you please advise on how to fix the error?

[Feb 27 16:57:26] Running TensorQTL: trans-QTL mapping

• WARNING: using CPU!
• reading phenotypes (TPMmatrix.tensorqtl_format.bed)
• reading covariates (covariance.matrix.txt)
• reading interaction term(s) (interaction.infol.txt)
• loading genotypes
  Mapping files: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 260.68it/s]
  trans-QTL mapping
• 287 samples
• 22447 phenotypes
• 1 covariates
• 1111 variants
• including interaction term
  tensorqtl/lib/python3.11/site-packages/tensorqtl/trans.py:188: FutureWarning: Series.getitem treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
  interaction_mask_t = torch.BoolTensor(mask_s).to(device)
  processing batch 1/1
  Traceback (most recent call last):
  File "", line 198, in _run_module_as_main
  File "", line 88, in _run_code
  File "tensorqtl/lib/python3.11/site-packages/tensorqtl/main.py", line 2, in
  tensorqtl.main()
  File "tensorqtl/lib/python3.11/site-packages/tensorqtl/tensorqtl.py", line 328, in main
  pairs_df = trans.map_trans(genotype_df, phenotype_df, covariates_df=covariates_df, interaction_s=interaction_df,
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "tensorqtl/lib/python3.11/site-packages/tensorqtl/trans.py", line 276, in map_trans
  res = calculate_interaction_nominal(genotypes_t, phenotypes_t, interaction_t, residualizer,
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py", line 189, in calculate_interaction_nominal
  i0_t = residualizer.transform(i0_t.t(), center=False).t()
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py", line 62, in transform
  M0_t = M_t - torch.mm(torch.mm(M0_t, self.Q_t), self.Q_t.t())
  ^^^^^^^^^^^^^^^^^^^^^^^^
  RuntimeError: mat1 and mat2 shapes cannot be multiplied (287x1 and 287x1)