search

broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
Other
557 stars 164 forks source link

infercnv::plot_cnv() takes too much time #583

Open wangziqi0321 opened 1 year ago

wangziqi0321 commented 1 year ago

@GeorgescuC Hi, thanks for developing this useful tool, yet I have encountered a problem:
I'm using infercnv on a dataset contained about 200k cells (20k in observation data and 180k in reference data). In the step

"Making the final infercnv heatmap",

the process stays at

"INFO [2023-08-11 23:36:48] plot_cnv_references:Start INFO [2023-08-11 23:36:48] Reference data size: Cells= 189435 Genes= 4738"

for over 30 hours, and is still running, I wonder if this is normal? Should I just keep on waiting? or there is something wrong with my code? Thanks!

infercnv_obj <- infercnv::run(infercnv_input, cutoff=0.1, min_cells_per_gene = 3, out_dir="cnv_output_dir_2", cluster_by_groups= T, plot_steps= F, mask_nonDE_genes = F, k_obs_groups = 1, hclust_method = "complete", denoise=T, output_format = "png", HMM=F, write_expr_matrix = T, num_threads=4 )

PS: The same step for observation data(20k cells) only takes less than one minute.

CHJCreateConvenience commented 6 months ago

I have the same situation. Have you solved it?