Is pyscenic grn proceeding? It does not throw any responses.

[hansong798]

Hello,
I'm running pyscenic using a docker container with data of 95121 cells * 28067 genes.

However, now it is running over two days and it does not throw any responses like below.

My code is:

docker run -it -v $PWD:$PWD aertslab/pyscenic:0.12.0 \
pyscenic grn \
--num_workers 30 \
--output adj.tsv \
--method grnboost2 \
--sparse \
fracture.loom \
hs_hgnc_tfs.txt

When I checked top command, it seemed like still running.
But it takes long time so I don't know whether I need to stop the process.
Is this running well? How long does it take to perform grnboost?

[ggruenhagen3]

Seems like its unclear to many how long the tool takes to run, as there are several threads about that on this github. Perhaps the developers should add a brief statement about memory and runtime to the docs to give users a rough idea. Looking around this github, here are a few responses from the dev team and other users on runtime:
#80 (comment)
#185 (comment)
#426 (includes comments on a 263159 cells x 14357 genes matrix, a 70k cell matrix, a 20k x 20k matrix, and a 80k+ x 30k matrix)
#217 (comment)

[Pentayouth]

add my experience here for those feeling anxious like me.
20000 genes * 20000 cells 30 core
9hr30min

[liezeltamon]

add my experience here for those feeling anxious like me.
20000 genes * 20000 cells 30 core
9hr30min

Thanks for sharing! @Pentayouth . How about memory usage? Also are you using Arboreto here?

[Pentayouth]

add my experience here for those feeling anxious like me.
20000 genes * 20000 cells 30 core
9hr30min

Thanks for sharing! @Pentayouth . How about memory usage? Also are you using Arboreto here?

@liezeltamon Hi, I am using the latest docker image. The memory usage is just fine on my 128GB desktop and allow me do other things. I dont quite remember exactly how much memory usage.