search

xtonyjiang / GNOVA

A principled framework to estimate annotation-stratified genetic covariance using GWAS summary statistics.
http://www.cell.com/ajhg/abstract/S0002-9297(17)30453-6
GNU General Public License v3.0
26 stars 13 forks source link

Program frozen for a long time without error/output #14

Open anbai106 opened 1 year ago

anbai106 commented 1 year ago

Hi,

Thanks for this tool.

I ran the code to estimate the rg between two traits, but the code got stuck for more than 3 hours, without outputting any files.

Preparing files for analysis... Calculating LD scores... ~/software/gnova/lib/python2.7/site-packages/numpy/core/fromnumeric.py:56: FutureWarning: Series.nonzero() is deprecated and will be removed in a future version.Use Series.to_numpy().nonzero() instead return getattr(obj, method)(*args, **kwds)

Is this normal???

Thanks

anbai106 commented 1 year ago

I think the step to calculating the LD scores from the reference panel is time-consuming.

Do you accept the pre-computed LD scores files from LDSC???

At least, the software does not have these arguments.

Thanks