ValueError: array must not contain infs or NaNs

[desindygogo]

Hello, I encountered the following error when performing permutation, there is no output, but there it seems normal in the log file , I would like to know what is the cause of this?
The same data works properly when using cis_nominal mode.

thanks!

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**ocessing phenotype 10391/10393^M processing phenotype 10392/10393WARNING: scipy.optimize.newton failed to converge (running scipy.optimize.minimize) ^M processing phenotype 10393/10393 Traceback (most recent call last): File "/share/home/zhuyunfei/miniconda3/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/share/home/zhuyunfei/miniconda3/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/share/home/zhuyunfei/miniconda3/lib/python3.9/site-packages/tensorqtl/main.py", line 2, in tensorqtl.main() File "/share/home/zhuyunfei/miniconda3/lib/python3.9/site-packages/tensorqtl/tensorqtl.py", line 141, in main calculate_qvalues(res_df, fdr=args.fdr, qvalue_lambda=args.qvalue_lambda, logger=logger) File "/share/home/zhuyunfei/miniconda3/lib/python3.9/site-packages/tensorqtl/post.py", line 40, in calculate_qvalues r = stats.pearsonr(res_df['pval_perm'], res_df['pval_beta'])[0] File "/share/home/zhuyunfei/miniconda3/lib/python3.9/site-packages/scipy/stats/_stats_py.py", line 4455, in pearsonr normym = linalg.norm(ym) File "/share/home/zhuyunfei/miniconda3/lib/python3.9/site-packages/scipy/linalg/_misc.py", line 145, in norm a = np.asarray_chkfinite(a) File "/share/home/zhuyunfei/miniconda3/lib/python3.9/site-packages/numpy/lib/function_base.py", line 628, in asarray_chkfinite raise ValueError( ValueError: array must not contain infs or NaNs WARNING: scipy.optimize.newton failed to converge (running scipy.optimize.minimize) Time elapsed: 10.47 min done.

• writing output Computing q-values

• Number of phenotypes tested: 10393**

[francois-a]

Please try this again with the latest commit.