RuntimeWarning: invalid value encountered in sqrt, and output pge with NaN value

[Steven-Shixq]

Hi, thanks for the useful package.

When I run the test file with this software it works fine until when processing my own data it outputs an error like:

RuntimeWarning: invalid value encountered in sqrt.

Could you give me any advice to solve this problem?

Here is the error log:

Popcorn version 1.0
(C) 2015-2019 Brielin C Brown
University of California, Berkeley
GNU General Public License v3

Invoking command: python /root/miniconda3/lib/python3.9/site-packages/popcorn/__main__.py fit -v 3 --cfile EUR_EAS_all_gen_eff.cscore --gen_effect --sfile1 EUR.txt --sfile2 EAS.txt out.txt
Beginning analysis at Wed Aug 31 20:06:51 2022
Analyzing a pair of traits in two populations
11916706 7376075 SNPs detected in input.
3552105 SNPs remaining after merging with score file.
3528699 SNPs remaining after filtering on AF and self-compliment SNPs.
/root/miniconda3/lib/python3.9/site-packages/popcorn/fit.py:288: RuntimeWarning: invalid value encountered in sqrt
  pg = P_Res(x=res_wls.params.values[1]/np.sqrt(h1.h_res.x[1]*h2.h_res.x[1]))
/root/miniconda3/lib/python3.9/site-packages/popcorn/fit.py:223: RuntimeWarning: invalid value encountered in sqrt
  hgr = pgr*np.sqrt(h1r*h2r)
Initial estimate:
       Val (obs)  SE
h1^2   0.031604 NaN
h2^2  -0.233816 NaN
pg          NaN NaN
Performing jackknife estimation of the standard error using 200 blocks of size 17643 .
Jackknife iter: 1 
/root/miniconda3/lib/python3.9/site-packages/popcorn/fit.py:288: RuntimeWarning: invalid value encountered in sqrt
  pg = P_Res(x=res_wls.params.values[1]/np.sqrt(h1.h_res.x[1]*h2.h_res.x[1]))
/root/miniconda3/lib/python3.9/site-packages/popcorn/fit.py:237: RuntimeWarning: invalid value encountered in sqrt
  hg = res[4].x*np.sqrt(res[0].h_res.x[1]*res[2].h_res.x[1])
Jackknife iter: 2 
/root/miniconda3/lib/python3.9/site-packages/popcorn/fit.py:288: RuntimeWarning: invalid value encountered in sqrt
  pg = P_Res(x=res_wls.params.values[1]/np.sqrt(h1.h_res.x[1]*h2.h_res.x[1]))
/root/miniconda3/lib/python3.9/site-packages/popcorn/fit.py:237: RuntimeWarning: invalid value encountered in sqrt
  hg = res[4].x*np.sqrt(res[0].h_res.x[1]*res[2].h_res.x[1])
Jackknife iter: 3 
/root/miniconda3/lib/python3.9/site-packages/popcorn/fit.py:288: RuntimeWarning: invalid value encountered in sqrt
  pg = P_Res(x=res_wls.params.values[1]/np.sqrt(h1.h_res.x[1]*h2.h_res.x[1]))
/root/miniconda3/lib/python3.9/site-packages/popcorn/fit.py:237: RuntimeWarning: invalid value encountered in sqrt
  hg = res[4].x*np.sqrt(res[0].h_res.x[1]*res[2].h_res.x[1])
  ...
  
        Val (obs)        SE          Z     P (Z)
h1^2   0.031604  0.002202  14.349459  0.000000
h2^2  -0.233816  0.343909  -0.679877  0.496582
pge         NaN       NaN        NaN       NaN
Analysis finished at Wed Aug 31 20:21:06 2022
Total time elapsed: 855.33

Please let me know if you need any more information.

Best,
Shixq

[yc-long]

I wonder if you have solved the problem now that I am also experiencing it.

[zasgel]

Hi I am having the same issue, has anyone found the solution?

[lanshanxuying]

Hi, I have had the same problem. I wonder is there any solution about this?