SNPweights Software ERROR

Question

[tamar.crum]

I am working with SNPweights software and am trying to calculate my own snp weights based on my reference set of individuals. To do so, I need the .evec, .eval, and .log outputs from SMARTPCA. I then run the calc_snpwt.py program and receive the following error:

Traceback (most recent call last): File "calc_snpwt.py", line 188, in <module> calculate_snpwt() File "calc_snpwt.py", line 172, in calculate_snpwt W = XV/(S2*trace) UnboundLocalError: local variable 'trace' referenced before assignment

I have done testing and have determined I am missing a value in my .log file that the program needs to run. Has anyone used the calc_snpwt.py program within the SNPweights software package?

Answer 1

[vadimverenich]

You're probably using the latest version of smartpca (EIGENSTRAT 6 or higher). I would suggest to run smartpca from the previous version, I used smartpca version: 10210 and it solved the issue