search

broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
Other
566 stars 166 forks source link

Error in step 17 #502

Open dbswls0322 opened 1 year ago

dbswls0322 commented 1 year ago

Hi I got some error running inferCNV

This is my code.

infercnv_obj = infercnv::run(infercnv_obj, cutoff=0.1, out_dir="output_dir", cluster_by_groups=T, denoise=T, HMM=T)

This is error that i got.

STEP 17: HMM-based CNV prediction

INFO [2023-02-14 09:18:04] predict_CNV_via_HMM_on_whole_tumor_samples INFO [2023-02-14 09:18:09] -done predicting CNV based on initial tumor subclusters INFO [2023-02-14 09:18:35] get_predicted_CNV_regions(subcluster) INFO [2023-02-14 09:18:35] -processing cell_group_name: 2_tumor.2_tumor_s1, size: 12640 INFO [2023-02-14 09:19:34] -processing cell_group_name: 1_normal.1_normal_s1, size: 1775 INFO [2023-02-14 09:19:47] -writing cell clusters file: output_dir/17_HMM_preds.cell_groupings INFO [2023-02-14 09:19:47] -writing cnv regions file: output_dir/17_HMM_preds.pred_cnv_regions.dat INFO [2023-02-14 09:19:47] -writing per-gene cnv report: output_dir/17_HMM_preds.pred_cnv_genes.dat INFO [2023-02-14 09:19:47] -writing gene ordering info: output_dir/17_HMM_preds.genes_used.dat INFO [2023-02-14 09:19:49] ::plot_cnv:Start INFO [2023-02-14 09:19:49] ::plot_cnv:Current data dimensions (r,c)=8387,14415 Total=373503015 Min=2 Max=4. INFO [2023-02-14 09:19:50] ::plot_cnv:Depending on the size of the matrix this may take a moment. Error in if (class(plot_data) %in% c("matrix", "data.frame")) { : the condition has length > 1

Because of this error, I couldn't get result file. I hope i can solve this problem.

I'll wait for your answer.

Have a nice day

GeorgescuC commented 1 year ago

Hi @dbswls0322 ,

The line of code where the error occurs has changed back in version 1.3.3, so the issue should likely be fixed in the current version if you update.

Regards, Christophe.

dbswls0322 commented 1 year ago

Thank you for replying.

I appreciate your help :)