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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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infercnv::run: Error in require_above_min_cells_ref(infercnv_obj, min_cells_per_gene = min_cells_per_gene) : 998 #555

Open Urja25 opened 1 year ago

Urja25 commented 1 year ago

I am trying to run inferCNV with the following code:

infercnv_obj = infercnv::run(infercnv_obj, cutoff=0.1, # use 1 for smart-seq, 0.1 for 10x-genomics min_cells_per_gene = 1, out_dir="/omics/groups/OE0585/internal/urja/infercnv/raw_data", # dir is auto-created for storing outputs cluster_by_groups=F, # cluster denoise=T, HMM=T, )

I get the following error message: INFO [2023-06-07 16:54:48] ::process_data:Start INFO [2023-06-07 16:54:48] Checking for saved results. INFO [2023-06-07 16:54:48] Trying to reload from step 2 INFO [2023-06-07 16:54:51] Trying to reload from step 1 INFO [2023-06-07 16:54:51] Using backup from step 1 INFO [2023-06-07 16:54:51] 

STEP 1: incoming data

INFO [2023-06-07 16:54:51] 

STEP 02: Removing lowly expressed genes

INFO [2023-06-07 16:54:51] ::above_min_mean_expr_cutoff:Start INFO [2023-06-07 16:54:51] Removed 30556 genes having fewer than 1 min cells per gene = 100 % genes removed here WARN [2023-06-07 16:54:51] ::All genes removed! Must revisit your data..., cannot continue here. Error in require_above_min_cells_ref(infercnv_obj, min_cells_per_gene = min_cells_per_gene) : 998

I am working with 10X data and I suppose that the data is extremely sparse since the dataset is from all healthy cells.

I set the min_cells_per_gene value to 0 but I got the following error:

Error in .normalize_data_matrix_by_seq_depth(data, normalize_factor) : Error, normalize factor not estimated

Can you please give me a hint as to what might be going wrong?

Thanks a lot!

GeorgescuC commented 1 year ago

Hi @Urja25 ,

Based on those errors, it seems like the matrix you are using as input is completely empty or has all 0s/NAs. Another option would be that there are no cells in the matrix because cell names do not match with the annotation file. Can you try running CreateInfercnvObject() again and post the log from that?

Regards, Christophe.