Error on Step 15: No feature overlap between existing object and new layer data

[r-osorio]

Hello,

Thank you for your wonderful product!

I am analyzing multiple datasets in parallel using a similar inferCNV code workflow. My datasets are integrated seurat objects which I have converted to inferCNV objects without issue. Four of my six datasets get through my workflow perfectly and without issue. Two of them however are throwing the same error on step 15 of my inferCNV analysis:

`STEP 15: computing tumor subclusters via leiden

INFO [2024-03-08 09:45:32] define_signif_tumor_subclusters(p_val=0.1
INFO [2024-03-08 09:45:35] define_signif_tumor_subclusters(), tumor: myTumor
INFO [2024-03-08 09:45:35] Setting auto leiden resolution for myTumor to 0.000278088
Error: No feature overlap between existing object and new layer data
Execution halted`

I am confused because all six datasets underwent the same preprocessing and clustering workflow before my cnv analysis (some even have the same cells - they are different combinations of integrated datasets). The only differences I can think of between datasets is the two that are throwing this error are by far the two largest datasets of the bunch.

Thanks for any help you can provide, I am stumped on how to troubleshoot this error since my other workflows ran successfully on the same code.

[kiritsugu233]

hey, I have the same problem. did you solve it?

[r-osorio]

no fix yet - tried rebuilding the cnv object from the raw data/from scratch and the same error occurs. Really not sure where to go from here...

[mortadelo93]

Same error here...

[mortadelo93]

Hey, I could fix it by simply changing cluster names.
I had clusters as numbers so gave them a character name. That fixed it...

[kiritsugu233]

I will try it. thank you mortadelo93 !!

[r-osorio]

All my samples already had cluster names as character strings. Will try renaming them to something else and running, @kiritsugu233 let me know if you have success. Thanks @mortadelo93

[sd68515]

I encountered the same problem. Finally, the numerical column names of the clusters in the read data were renamed to the corresponding cell type names.