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(myenv27) C:\Users\danty\Dropbox\hess\h>python hess.py --prefix step1h_trait1 --out step2h_trait1
[INFO] Command started at: Fri, 09 Feb 2018 16:47:45
[INFO] Command issued:
hess.py
--prefix step1h_trait1
--out step2h_trait1
[INFO] Loaded results for 1568 loci from step 1
[INFO] Using 4133481 SNPs with average sample size 77096.0
[INFO] Re-inflate the summary statistics with lambda_gc: 1
[INFO] Total SNP-heritability estimate: 0.606 (0.00698)
Traceback (most recent call last):
File "hess.py", line 217, in
main()
File "hess.py", line 40, in main
argmap['gwse-thres'], argmap['tot-hsqg'], argmap['out'])
File "C:\Users\danty\Dropbox\hess\h\src\estimation.py", line 174, in local_hsqg_step2
min_eigval, reinflate, gwse_thres)
File "C:\Users\danty\Dropbox\hess\h\src\estimation.py", line 285, in local_hsqg_step2_helper
se = np.sqrt(local_hsqg_est_var)
AttributeError: 'float' object has no attribute 'sqrt'

Ah! Yes, thank you! I was using latest versions of packages, but I downgraded to nearest available and this solved the problem.

matplotlib: 2.1.2-py27ha51faf0_0  --> 1.4.3-np110py27_3
mkl:        2018.0.1-h2108138_4   --> 11.3.1-0
numpy:      1.14.0-py27hfef472a_1 --> 1.10.4-py27_0
pandas:     0.22.0-py27hc56fc5f_0 --> 0.18.1-np110py27_0
pyqt:       5.6.0-py27h224ed30_5  --> 4.10.4-py27_1
scipy:      1.0.0-py27h7cd1477_0  --> 0.16.1-np110py27_1