I have been trying SCENIC on our data and got the error message mentioned in the title. The dataset I am using is a 22057 17057 matrix processed by scanpy package. If I use the whole matrix then it give me the error, however, if I only use part of the matrix (1000017057), then it can be finished. At first I thought it is memory issue, but I am using a cluster with 128Gb memory and SCENIC only takes 32Gb before it shows the error. Thus, I have two questions here:
Please advice me on how to solve this error
If I chop the matrix into pieces and run GRNboost on each piece to get regulon and then take the union and run aucell. Does it equal to run GRNboost on whole matrix and then apply resulted regulon to aucell?
The detailed code and error message is shown below.
Hello,
I have been trying SCENIC on our data and got the error message mentioned in the title. The dataset I am using is a 22057 17057 matrix processed by scanpy package. If I use the whole matrix then it give me the error, however, if I only use part of the matrix (1000017057), then it can be finished. At first I thought it is memory issue, but I am using a cluster with 128Gb memory and SCENIC only takes 32Gb before it shows the error. Thus, I have two questions here:
The detailed code and error message is shown below.
Thanks