cuelee
commented
2 years ago Thanks for letting me know the issue.
Yes, I was also interested in the issues you reported. This problem usually occurs when the versions of Python dependencies such as Numpy or Pandas do not match. Today, I released a new version that addressed most of these issues. The simplest way to use the latest version is to download and install PLEIO again. The latest version has a .py extension in the executable, so you have to be careful when using it.
Best Regards, Cue Hyunkyu Lee
RaviBot
Hi there! First off, thank you so much for making this software available to the public. I am getting an error when running the tutorial data. I've tried it on a server and local system so I'm not sure how to get past it. Any help would be much appreciated. Thanks in advance!
`(pleio) -bash-4.2$ ./pleio --metain example/input.txt.gz --sg example/sg.txt.gz --ce example/re.txt.gz --nis 100000 --parallel --create --out example/output
Call: ./pleio.py \ --out example/output \ --metain example/input.txt.gz \ --sg example/sg.txt.gz \ --ce example/re.txt.gz \ --create \ --parallel
Beginning analysis at Wed Jan 5 15:40:12 2022 genetic covariance matrix is not a positive definite matrix Analysis finished at Wed Jan 5 15:40:14 2022 Total time elapsed: Traceback (most recent call last): File "./pleio", line 264, in
pleio(args,log)
File "./pleio", line 180, in pleio
meta_cain.zero_prob = importance_sampling(args.nis, meta_cain.N_gwas, meta_cain.Sg, meta_cain.Ce, importance_sampling_f, args.ncores);
File "/ifs/loni/faculty/njahansh/nerds/ravi/pleio/framework/importance_sampling.py", line 214, in importance_sampling
Uinv_sqrt = sqrt_ginv(U);
File "/ifs/loni/faculty/njahansh/nerds/ravi/pleio/framework/importance_sampling.py", line 69, in sqrt_ginv
u, s, vt = np.linalg.svd(a, full_matrices=False, hermitian=True)
TypeError: svd() got an unexpected keyword argument 'hermitian'`