17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat file is empty

broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq

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17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat file is empty #394

Closed raybueno closed 2 years ago

raybueno commented 2 years ago

Hello,

I ran inferCNV to completion, however when reading in the 17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat file it is empty. The file just has the column names - (cell_group_name | gene_region_name | state | gene | chr | start | end) but no values in the rows. Why is this file empty? I am using infercnv version 1.11.2. Thank you.

GeorgescuC commented 2 years ago

Hi @raybueno ,

If you look at the HMM png/pdf figures, do you see any predicted CNVs? Do the residual expression figures have signal?

Regards, Christophe.

raybueno commented 2 years ago

Hi Christophe,

Yes I do see predicted CNVS from the png figure. I was hoping to see what the regions are predicted to have CNV using the files mentioned however these files are empty.

GeorgescuC commented 2 years ago

Hi @raybueno ,

Could you privately share with me the infercnv outputs from steps 15 and 17 so I can explore the issue? (my email can be found in the DESCRIPTION file)

Regards, Christophe.