Closed schroeme closed 3 months ago
Hi,
The most likely reason is your file is too large. I once applied scDRS to a dataset with 500K and it needed 96G of memory. I suggest:
Hi @martinjzhang, thanks so much for the quick response! I have 256G RAM on my computer, so I should be able to allocate 128G easily. Is the memory allocation something I can change when calling compute-score
? If not, how can I change it? Thanks!
Hi,
Allocating RAM to software should be done in the OS instead of within scDRS. Can you check to see if your system already allocate all memories to this program or it sets an upper limit?
Also, did you store your single-cell data in sparse format? Specifically, is adata.X
a sparse matrix? If not, converting it to a sparse matrix will further save memories.
Sparsifying adata.X (converting to raw counts) worked! Thank you!
Hello, I'm running scdrs
compute-score
per the instructions here, and I get the following error:My data is already log1p-transformed on normalized counts. Any idea what might be causing this error? Is the file size too large, or am I violiting any input requirements (I couldn't find any)?
Thanks!