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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Tutorial Error #445

Open e-arslan opened 2 years ago

e-arslan commented 2 years ago

When I try to run example code, I get the following error:

     infercnv_obj_default = infercnv::run(
            infercnv_obj,
            cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
            out_dir=out_dir,
            cluster_by_groups=TRUE, 
            plot_steps=FALSE,
            denoise=TRUE,
            HMM=FALSE,
            no_prelim_plot=TRUE,
           png_res=60
       )

STEP 15: computing tumor subclusters via leiden

INFO [2022-08-22 09:26:54] define_signif_tumor_subclusters(p_val=0.1 INFO [2022-08-22 09:26:54] define_signif_tumor_subclusters(), tumor: malignant_93 Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |================================================================================================| 100% Error in irlba(A = t(x = object), nv = npcs, ...) : max(nu, nv) must be strictly less than min(nrow(A), ncol(A))

GeorgescuC commented 2 years ago

Hi @e-arslan ,

Thanks for reporting the issue. This is due to the example dataset being small and the new changes to how we run the Leiden subclustering first running a PCA which tries to calculate too many PCs for this dataset size (and more than we use). I have updated the settings used, so if you reinstall from the master branch, the error should not happen anymore.

Regards, Christophe.