cell_groupings files are not created

Good day,

I want to get the . cell_groupings files but after running:

infercnv_obj = infercnv::run(infercnv_obj,
                             cutoff=0.1,  
                             out_dir="output",  
                             cluster_by_groups=F,  
                             analysis_mode="subclusters",
                             denoise=T,
                             HMM=T,
                             num_threads = 12
                             )

The file 2 hours ago281 MB HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_genes.dat is in the output directory, but not any cell_groupings files. The dat file looks like:

cell_group_name gene_region_name    state   gene    chr start   end
all_observations.all_observations.1.1.1.1   1-region_2  2   HSPG2   1   21678298    21783606
all_observations.all_observations.1.1.1.1   1-region_2  2   CDC42   1   21822245    21937297
all_observations.all_observations.1.1.1.1   1-region_2  2   C1QA    1   22052627    22092946
all_observations.all_observations.1.1.1.1   1-region_2  2   C1QC    1   22636506    22639608
all_observations.all_observations.1.1.1.1   1-region_2  2   C1QB    1   22643630    22648110
all_observations.all_observations.1.1.1.1   1-region_2  2   KDM1A   1   22652762    22661538
all_observations.all_observations.1.1.1.1   1-region_2  2   LUZP1   1   23019443    23083689
all_observations.all_observations.1.1.1.1   1-region_2  2   HNRNPR  1   23084023    23177808
all_observations.all_observations.1.1.1.1   1-region_2  2   ID3 1   23303771    23344336
all_observations.all_observations.1.1.1.1   1-region_2  2   RPL11   1   23557918    23559794
all_observations.all_observations.1.1.1.1   1-region_2  2   ELOA    1   23691742    23696835
all_observations.all_observations.1.1.1.1   1-region_2  2   PITHD1  1   23743155    23762059
all_observations.all_observations.1.1.1.1   1-region_2  2   LYPLA2  1   23778405    23788232
all_observations.all_observations.1.1.1.1   1-region_2  2   GALE    1   23790970    23795539
all_observations.all_observations.1.1.1.1   1-region_2  2   HMGCL   1   23795599    23800804
all_observations.all_observations.1.1.1.1   1-region_2  2   FUCA1   1   23801885    23838620
all_observations.all_observations.1.1.1.1   1-region_2  2   PNRC2   1   23845077    23868294
all_observations.all_observations.1.1.1.1   1-region_2  2   SRSF10  1   23959109    23963462
all_observations.all_observations.1.1.1.1   1-region_2  2   NIPAL3  1   23964804    23980927
all_observations.all_observations.1.1.1.1   1-region_2  2   RCAN3   1   24415794    24472976
all_observations.all_observations.1.1.1.1   1-region_2  2   SRRM1   1   24502351    24541040
all_observations.all_observations.1.1.1.1   1-region_2  2   CLIC4   1   24631716    24673267
all_observations.all_observations.1.1.1.1   1-region_2  2   SYF2    1   24745357    24844324
all_observations.all_observations.1.1.1.1   1-region_2  2   RSRP1   1   25222679    25232502
all_observations.all_observations.1.1.1.1   1-region_2  2   TMEM50A 1   25242237    25338213
all_observations.all_observations.1.1.1.1   1-region_2  2   MACO1   1   25337917    25362361
all_observations.all_observations.1.1.1.1   1-region_2  2   MAN1C1  1   25430858    25500209
all_observations.all_observations.1.1.1.1   1-region_2  2   SELENON 1   25617468    25786207
all_observations.all_observations.1.1.1.1   1-region_2  2   MTFR1L  1   25800176    25818224
all_observations.all_observations.1.1.1.1   1-region_2  2   STMN1   1   25818640    25832942
all_observations.all_observations.1.1.1.1   1-region_2  2   ZNF593  1   25884181    25906991
all_observations.all_observations.1.1.1.1   1-region_2  2   SH3BGRL3    1   26169871    26170873

The HMM plot looks like this:

Could you help me with that, please?

I am running the last version of infercnv (v1.7.1).

Thanks in advance

broadinstitute / infercnv

cell_groupings files are not created #279