Conditional cis-QTL Mapping Errors in tensorQTL

[MinS1]

Hi,

I am currently using tensorQTL to perform conditional cis-QTL mapping, but I am encountering multiple warnings and errors during the process. Specifically, I am seeing the following runtime warnings in the error log file:

/envs/tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py:370:
RuntimeWarning: divide by zero encountered in log
np.log(dof_init), tol=tol, maxiter=50)
/envs/tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py:340:
RuntimeWarning: invalid value encountered in divide
tstat2 = dof * r2 / (1 - r2)
/envs/tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py:340:
RuntimeWarning: divide by zero encountered in divide
tstat2 = dof * r2 / (1 - r2)
/envs/tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py:355:
RuntimeWarning: divide by zero encountered in log
return (1.0-shape1)*np.sum(np.log(x)) + (1.0-shape2)*np.sum(np.log(1.0-x)) + len(x)*logbeta
/envs/tensorqtl/lib/python3.11/site-packages/scipy/optimize/_optimiz
e.py:835: RuntimeWarning: invalid value encountered in subtract
np.max(np.abs(fsim[0] - fsim[1:])) <= fatol):
/envs/tensorqtl/lib/python3.11/site-packages/tensorqtl/cis.py:571: R
untimeWarning: divide by zero encountered in scalar divide
slope_se = np.abs(slope) / np.sqrt(tstat2)
/envs/tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py:370:
RuntimeWarning: invalid value encountered in log
np.log(dof_init), tol=tol, maxiter=50)
/envs/tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py:340:
RuntimeWarning: divide by zero encountered in divide
tstat2 = dof * r2 / (1 - r2)
/envs/tensorqtl/lib/python3.11/site-packages/tensorqtl/core.py:341:
RuntimeWarning: invalid value encountered in sqrt
......
......
......

These warnings appear for every chromosome, though the number of warnings varies across chromosomes. Despite the warnings, the conditional cis-QTL still produces result files. However, I have noticed that some of the pairs in the permutation result files are not present in the conditional cis-QTL result files. This leads me to believe that the warnings may be affecting the final results.

I would appreciate your guidance on how to resolve these issues. I have already confirmed that I am using the latest version of tensorQTL, and I am working with methylation data that does not contain missing values.

Could you please advise on the possible causes of these errors and how I can fix the issue to ensure more reliable results?

Thank you very much for your help!

Best regards,
Shi

[francois-a]

Can you please share a small test dataset that reproduces these errors?