Question about pyscenic run time and memory usage, and potential updates to workflow?

[liezeltamon]

Hi @Amelie-TGHN,

Thank you so much for your pyscenic workflow! Helped me a lot to quickly apply it to my dataset. It's from 2 years ago and just wondering whether you would recommend some changes to that workflow? Also, for the dataset that you used in that workflow, can you still remember roughly how long it took (particularly the first two steps) and the memory usage?

Thank you!

[Amelie-TGHN]

Hi @liezeltamon,
Glad it helped! I have not used pyscenic since I wrote this workflow, so I can unfortunately not advise regarding potential updates... From my notes, it seems the first 2 steps took ~16h in total for a 50k cells x 20k genes dataset, using 20 cores and 180G of memory.

[liezeltamon]

Hi @Amelie-TGHN, thanks for the reply! It seems that the new version then is more compute-intensive as some people have noted. I have about the same number of cells and genes but I can't even run it with more than 10 cores given 200G memory.

Thank you!