search

CHPGenetics / GMM-Demux

MIT License
13 stars 5 forks source link

GMM cannot find a viable solution that satisfies the droplet formation model. SSM rate estimation terminated. #6

Closed VitorAguiar closed 1 year ago

VitorAguiar commented 2 years ago

I get this error when using the -u option. Are there any options I could try?

Thank you!

$ GMM-demux filtered_feature_bc_matrix Hashtag1,Hashtag2,Hashtag3,Hashtag4,Hashtag5,Hashtag6 -u 13946                     
==============================GMM-Demux Initialization==============================
Confidence threshold: 0.8
Output directory: SSD_mtx
MSM-free droplets are stored in folder SSD_mtx 

GMM cannot find a viable solution that satisfies the droplet formation model. SSM rate estimation terminated.
xhongyi commented 2 years ago

Was 13946 the number of cells loaded to 10X or the number of cells harvested from the data? Were you using 10X Chromium or Chromium X? GMM-Demux's SSM inference system were tuned for Chromium not Chromium X. Could you provide the classification summary (how many singlets and doublets in total for each category)?

Thanks!

xhongyi commented 2 years ago

If you are out of options, you could also check out the GMM-Demux experiment planner at: http://54.152.221.82/exp_planner/

If you feed it with the loaded cell population size, it should be able to provide a rough estimation of the amount of total doublets.

Here I've made a screen shot of it. I'm not sure if it matches your results.

image