Open davidecrs opened 3 years ago
Hello. Enen. We havn't the issue. Thanks your 'problem'. Please show your whole pipeline and the error message.
Hi,
I have cloned this repo, installed the dependencies and I am trying scGCO package through the tutorial jupyter notebook, however there seems to be a problem with the execution. In particular, it happens to me that step 2 of that file is stucked in an infinite execution loop (on the function
gmmDict = multiGMM (data_norm)
). This seems to be confirmed by the HTOP panel where the scGCO processes are in theS
state.
Hello. Enen. We havn't the issue. Thanks your 'problem'. Please show your whole pipeline and the error message.
The code doesn't show any error message. It remains running for a long (too) long time, probably for an infinite time given the S state of the processes shown in the HTOP panel.
I simply executed the code in this tutorial without changing it https://github.com/WangPeng-Lab/scGCO/blob/master/code/Tutorial/scGCO_tutorial.ipynb .
The execution get stuck when running the fifth iteration (when tqdm progress bar shows 4/8 ) of gmmDict=multiGMM(data_norm)
(in step 2).
The code doesn't show any error message. It remains running for a long (too) long time, probably for an infinite time given the S state of the processes shown in the HTOP panel.
I simply executed the code in this tutorial without changing it https://github.com/WangPeng-Lab/scGCO/blob/master/code/Tutorial/scGCO_tutorial.ipynb . The execution get stuck when running the fifth iteration (when tqdm progress bar shows 4/8 ) of
gmmDict=multiGMM(data_norm)
(in step 2).
enen. Do you run our scGCO on windows ? Maybe the parallel have poor compatibility on windows.
You can direct run gmmDict = gmm_model(data_norm)
. without parallel. In addition, You can save time gmmDict = gmm_model(data_norm.loc[:,your_geneList]).
I run scGCO on Ubuntu 20.04 with python 3.8.5.
Thanks for your help, with gmmDict = gmm_model(data_norm)
it works !
Hi,
I have cloned this repo, installed the dependencies and I am trying scGCO package through the tutorial jupyter notebook, however there seems to be a problem with the execution. In particular, it happens to me that step 2 of that file is stucked in an infinite execution loop (on the function
gmmDict = multiGMM (data_norm)
). This seems to be confirmed by the HTOP panel where the scGCO processes are in theS
state.