I am trying to use Supergnova (https://github.com/YiliangTracyZhang/SUPERGNOVA) to calculate local genetic correlations from multiple GWAS summary statistics. To start with, I'm trying to run the tutorial they provide, but the final command:
python3 supergnova.py ./data/sumstats/ASD.txt.sumstats.gz ./data/sumstats/CP.txt.sumstats.gz \ --N1 46351 \ --N2 257828 \ --bfile data/bfiles/eur_chr@_SNPmaf5 \ --partition data/partition/eur_chr@.bed \ --out results.txt
gets stuck without showing any error after it has been running for more than 24 hours. From what I have read, the expected process time is between 30 min and 1 hour, which clearly suggests that something is not working properly.
I have created a conda environment with the packages required to use Supergnova (Python 3, numpy scipy, pandas, sklearn, bitarray) but since there are no previous steps and I am simply following all the steps in the tutorial, I don't know what might be going on. I would appreciate if someone could suggest me something I could try to do to solve it.