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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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error during HMM prediction without reference cells #635

Open Mashuaiii opened 8 months ago

Mashuaiii commented 8 months ago

Hi GeorgescuC, thank you for this useful tool! I am working with R version 4.3.2 and infercnv 1.18.1 but I can't be able to obtain prediction with HMM model. I obtained this error:

STEP 17: HMM-based CNV prediction

INFO [2024-01-22 09:55:23] i3HMM_predict_CNV_via_HMM_on_tumor_subclusters(i3_p_val=0.05, use_KS=FALSE) INFO [2024-01-22 09:55:23] determine mean delta (sigma: NA, p=0.05) -> NA mean_delta: NA, at sigma: NA, and pval: 0.05 WARN [2024-01-22 09:55:23] get_HoneyBADGER_setGexpDev:: k_cells must be at least 2, setting to 2 Error in seq.default(0, gexp.sd, gexp.sd/10) : 'to' must be a finite number

Is it possible to apply i3HMM model without reference cells in infercnv 1.18.1? However, I found i6HMM model can apply without reference cell.

Thank you so much.