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qlu-lab / SUPERGNOVA

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Problem with tutorial #10

Open Gerardts9 opened 2 years ago

Gerardts9 commented 2 years ago

I am trying to run the tutorial, but the final command, where supergnova.py is called, gets stuck at the following message:

"24 CPUs are detected. Using 24 threads in computation ..."

without showing any error after it has been running for more than 24 hours.

I have created a conda environment with the required packages to run the commands, but I don't know what might be going on. I suspect the problem could be that I am not using the right package versions, as it happens with the pandas newest version. I would be very grateful if you could help me to know what is causing this.

Thanks.

nrs225 commented 1 year ago

Hi. I also have this same problem with running the tutorial.

No output or error messages are generated after this point:

Calculating phenotypic correlation...
Calculating local genetic covariance...
44 CPUs are detected. Using 44 threads in computation  ...

The job keeps running until it times out after 2 days, but it doesn't appear to be doing anything during this time.

Thanks.

Gerardts9 commented 1 year ago

Hi,

@nrs225 I managed to solve the problem changing the versions of the Python packages SUPERGNOVA requires. I let them noted here in case you want to give it a try:

Numpy 1.19.5 Scipy 1.5.4 pandas 0.25.3 bitarray 2.1.0 sklearn = scikit-learn 0.24.2

Gerardts9 commented 8 months ago

Hi @nvice111,

I am still using the same versions for the packages and Python.

For the SUPERGNOVA environment, I am using Python 3.7.13.

The complete list of packages for the environment is the following:

Package Version

bitarray 2.1.0 certifi 2022.6.15 joblib 1.1.0 numpy 1.19.5 pandas 0.25.3 pip 22.1.2 python-dateutil 2.8.2 pytz 2022.1 scikit-learn 0.24.2 scipy 1.5.4 setuptools 58.0.4 six 1.16.0 threadpoolctl 3.1.0 wheel 0.37.1

Gerardts9 commented 8 months ago

Hi,

I just run this step from the tutorial:

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

on my server using 56 threads, and it took around 2 hours to complete for ALL the chromosomes.

Regarding the results, I checked that region on chromosome one, and my p-value is also slightly different from the Supplementary Table and yours (p-value = 1.8681e-05), but I think they are similar enough not to indicate a problem.