Error in .plot_cnv_references(ref_data = ref_data_t, ref_groups = ref_groups, : with R version 4.1.2 but same code working with R version 4.1.0 if I put cluster_by_groups=FALSE

[SaritaPoonia]

STEP 17: HMM-based CNV prediction

INFO [2022-03-26 18:59:57] predict_CNV_via_HMM_on_whole_tumor_samples INFO [2022-03-26 19:00:01] -done predicting CNV based on initial tumor subclusters INFO [2022-03-26 19:00:32] get_predicted_CNV_regions(subcluster) INFO [2022-03-26 19:00:32] -processing cell_group_name: all_observations.all_observations_s1, size: 4202 INFO [2022-03-26 19:01:21] -processing cell_group_name: all_references.all_references_s1, size: 5000 INFO [2022-03-26 19:02:15] -writing cell clusters file: /home/saritap/Clonal_fitness/infercnv/17_HMM_predHMMi6.hmm_mode-samples.cell_groupings INFO [2022-03-26 19:02:15] -writing cnv regions file: /home/saritap/Clonal_fitness/infercnv/17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_regions.dat INFO [2022-03-26 19:02:15] -writing per-gene cnv report: /home/saritap/Clonal_fitness/infercnv/17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat INFO [2022-03-26 19:02:15] -writing gene ordering info: /home/saritap/Clonal_fitness/infercnv/17_HMM_predHMMi6.hmm_mode-samples.genes_used.dat INFO [2022-03-26 19:02:17] ::plot_cnv:Start INFO [2022-03-26 19:02:17] ::plot_cnv:Current data dimensions (r,c)=16172,9202 Total=446444232 Min=3 Max=3. INFO [2022-03-26 19:02:17] ::plot_cnv:Depending on the size of the matrix this may take a moment. INFO [2022-03-26 19:03:52] plot_cnv_observation:Start INFO [2022-03-26 19:03:52] Observation data size: Cells= 4202 Genes= 16172 INFO [2022-03-26 19:03:53] plot_cnv_observation:Writing observations by grouping. INFO [2022-03-26 19:04:36] plot_cnv_observation:Writing observation groupings/color. INFO [2022-03-26 19:04:36] plot_cnv_observation:Done writing observation groupings/color. INFO [2022-03-26 19:04:37] plot_cnv_observation:Writing observation heatmap thresholds. INFO [2022-03-26 19:04:37] plot_cnv_observation:Done writing observation heatmap thresholds. INFO [2022-03-26 19:04:45] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000 INFO [2022-03-26 19:04:45] Quantiles of plotted data range: 3,3,3,3,3 INFO [2022-03-26 19:04:50] plot_cnv_observations:Writing observation data to /home/saritap/Clonal_fitness/infercnv/infercnv.17_HMM_predHMMi6.hmm_mode-samples.observations.txt INFO [2022-03-26 19:05:33] plot_cnv_references:Start INFO [2022-03-26 19:05:33] Reference data size: Cells= 5000 Genes= 16172 ERROR [2022-03-26 19:05:33] Unexpected error, should not happen. Error in .plot_cnv_references(ref_data = ref_data_t, ref_groups = ref_groups, : Error

R version _
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 1.2
year 2021
month 11
day 01
svn rev 81115
language R
version.string R version 4.1.2 (2021-11-01) nickname Bird Hippie

[GeorgescuC]

Hi @SaritaPoonia ,

Did the plotting run properly at step 15, where the preliminary output should be generated, or did you disable the plotting at that step?

This is an unexpected behavior because the error message you get should not be possible to reach in the case where you are running infercnv with cluster_by_groups=FALSE and thus references are all grouped under "all_references".

Could you let me know which version of infercnv you are using for both R versions? There might be a difference there based on which version of BioConductor is available. Also, was the run on R 4.1.2 started from scratch, or is it using backups from object generated under R 4.1.0?

As a side note, running the HMM in samples mode without any subclustering is only recommanded if there is no clonal diversity within your data, which you can confirm by looking at the residual expression plots.

Regards, Christophe.