> dir.create("plot_out2")#新建，原来没有这个文件夹
> infercnv_obj1 = infercnv::run(infercnv_obj,
+ cutoff=0.1,
+ out_dir= 'plot_out2' ,
+ cluster_by_groups=TRUE,
+ denoise=TRUE,#默认false
+ HMM=TRUE)#默认false
INFO [2021-03-11 11:00:09] ::process_data:Start
INFO [2021-03-11 11:00:09] Checking for saved results.
INFO [2021-03-11 11:00:09]
STEP 1: incoming data
INFO [2021-03-11 11:00:09]
STEP 02: Removing lowly expressed genes
INFO [2021-03-11 11:00:09] ::above_min_mean_expr_cutoff:Start
INFO [2021-03-11 11:00:09] Removing 5199 genes from matrix as below mean expr threshold: 0.1
INFO [2021-03-11 11:00:09] validating infercnv_obj
INFO [2021-03-11 11:00:09] There are 2758 genes and 161 cells remaining in the expr matrix.
INFO [2021-03-11 11:00:09] no genes removed due to min cells/gene filter
INFO [2021-03-11 11:00:09]
STEP 03: normalization by sequencing depth
INFO [2021-03-11 11:00:09] normalizing counts matrix by depth
INFO [2021-03-11 11:00:09] Computed total sum normalization factor as median libsize: 1424.000000
INFO [2021-03-11 11:00:09] Adding h-spike
INFO [2021-03-11 11:00:09] -hspike modeling of ref-fib
INFO [2021-03-11 11:01:11] validating infercnv_obj
INFO [2021-03-11 11:01:11] normalizing counts matrix by depth
INFO [2021-03-11 11:01:11] Using specified normalization factor: 1424.000000
INFO [2021-03-11 11:01:12]
STEP 04: log transformation of data
INFO [2021-03-11 11:01:12] transforming log2xplus1()
INFO [2021-03-11 11:01:12] -mirroring for hspike
INFO [2021-03-11 11:01:12] transforming log2xplus1()
INFO [2021-03-11 11:01:13]
STEP 08: removing average of reference data (before smoothing)
INFO [2021-03-11 11:01:13] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 11:01:13] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 11:01:14] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 11:01:15] -mirroring for hspike
INFO [2021-03-11 11:01:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 11:01:15] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 11:01:17] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 11:01:19]
STEP 09: apply max centered expression threshold: 3
INFO [2021-03-11 11:01:19] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2021-03-11 11:01:19] -mirroring for hspike
INFO [2021-03-11 11:01:19] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2021-03-11 11:01:20]
STEP 10: Smoothing data per cell by chromosome
INFO [2021-03-11 11:01:20] smooth_by_chromosome: chr: chr1
INFO [2021-03-11 11:01:20] smooth_by_chromosome: chr: chr10
INFO [2021-03-11 11:01:21] smooth_by_chromosome: chr: chr11
INFO [2021-03-11 11:01:21] smooth_by_chromosome: chr: chr12
INFO [2021-03-11 11:01:21] smooth_by_chromosome: chr: chr13
INFO [2021-03-11 11:01:21] smooth_by_chromosome: chr: chr14
INFO [2021-03-11 11:01:21] smooth_by_chromosome: chr: chr15
INFO [2021-03-11 11:01:22] smooth_by_chromosome: chr: chr16
INFO [2021-03-11 11:01:22] smooth_by_chromosome: chr: chr17
INFO [2021-03-11 11:01:23] smooth_by_chromosome: chr: chr18
INFO [2021-03-11 11:01:23] smooth_by_chromosome: chr: chr19
INFO [2021-03-11 11:01:23] smooth_by_chromosome: chr: chr2
INFO [2021-03-11 11:01:23] smooth_by_chromosome: chr: chr20
INFO [2021-03-11 11:01:23] smooth_by_chromosome: chr: chr21
INFO [2021-03-11 11:01:23] smooth_by_chromosome: chr: chr22
INFO [2021-03-11 11:01:23] smooth_by_chromosome: chr: chr3
INFO [2021-03-11 11:01:24] smooth_by_chromosome: chr: chr4
INFO [2021-03-11 11:01:24] smooth_by_chromosome: chr: chr5
INFO [2021-03-11 11:01:24] smooth_by_chromosome: chr: chr6
INFO [2021-03-11 11:01:24] smooth_by_chromosome: chr: chr7
INFO [2021-03-11 11:01:25] smooth_by_chromosome: chr: chr8
INFO [2021-03-11 11:01:25] smooth_by_chromosome: chr: chr9
INFO [2021-03-11 11:01:26] -mirroring for hspike
INFO [2021-03-11 11:01:26] smooth_by_chromosome: chr: chrA
INFO [2021-03-11 11:01:26] smooth_by_chromosome: chr: chr_0
INFO [2021-03-11 11:01:27] smooth_by_chromosome: chr: chr_B
INFO [2021-03-11 11:01:27] smooth_by_chromosome: chr: chr_0pt5
INFO [2021-03-11 11:01:27] smooth_by_chromosome: chr: chr_C
INFO [2021-03-11 11:01:28] smooth_by_chromosome: chr: chr_1pt5
INFO [2021-03-11 11:01:28] smooth_by_chromosome: chr: chr_D
INFO [2021-03-11 11:01:28] smooth_by_chromosome: chr: chr_2pt0
INFO [2021-03-11 11:01:29] smooth_by_chromosome: chr: chr_E
INFO [2021-03-11 11:01:29] smooth_by_chromosome: chr: chr_3pt0
INFO [2021-03-11 11:01:29] smooth_by_chromosome: chr: chr_F
INFO [2021-03-11 11:01:32]
STEP 11: re-centering data across chromosome after smoothing
INFO [2021-03-11 11:01:32] ::center_smooth across chromosomes per cell
INFO [2021-03-11 11:01:32] -mirroring for hspike
INFO [2021-03-11 11:01:32] ::center_smooth across chromosomes per cell
INFO [2021-03-11 11:01:34]
STEP 12: removing average of reference data (after smoothing)
INFO [2021-03-11 11:01:34] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 11:01:34] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 11:01:35] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 11:01:35] -mirroring for hspike
INFO [2021-03-11 11:01:35] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 11:01:35] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 11:01:38] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 11:01:40]
STEP 14: invert log2(FC) to FC
INFO [2021-03-11 11:01:40] invert_log2(), computing 2^x
INFO [2021-03-11 11:01:40] -mirroring for hspike
INFO [2021-03-11 11:01:40] invert_log2(), computing 2^x
INFO [2021-03-11 11:01:42]
STEP 15: Clustering samples (not defining tumor subclusters)
INFO [2021-03-11 11:01:42] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-03-11 11:01:42] define_signif_tumor_subclusters(), tumor: epi
INFO [2021-03-11 11:01:42] cut tree into: 1 groups
INFO [2021-03-11 11:01:42] -processing epi,epi_s1
INFO [2021-03-11 11:01:42] define_signif_tumor_subclusters(), tumor: ref-fib
INFO [2021-03-11 11:01:42] cut tree into: 1 groups
INFO [2021-03-11 11:01:42] -processing ref-fib,ref-fib_s1
INFO [2021-03-11 11:01:42] -mirroring for hspike
INFO [2021-03-11 11:01:42] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-03-11 11:01:42] define_signif_tumor_subclusters(), tumor: spike_tumor_cell_ref-fib
INFO [2021-03-11 11:01:43] cut tree into: 1 groups
INFO [2021-03-11 11:01:43] -processing spike_tumor_cell_ref-fib,spike_tumor_cell_ref-fib_s1
INFO [2021-03-11 11:01:43] define_signif_tumor_subclusters(), tumor: simnorm_cell_ref-fib
INFO [2021-03-11 11:01:43] cut tree into: 1 groups
INFO [2021-03-11 11:01:43] -processing simnorm_cell_ref-fib,simnorm_cell_ref-fib_s1
INFO [2021-03-11 11:01:46] ::plot_cnv:Start
INFO [2021-03-11 11:01:46] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=444261.448584115 Min=0.7259085460275 Max=1.27974740879628.
INFO [2021-03-11 11:01:46] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 11:01:48] plot_cnv(): auto thresholding at: (0.882791 , 1.118216)
INFO [2021-03-11 11:01:48] plot_cnv_observation:Start
INFO [2021-03-11 11:01:48] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 11:01:48] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 11:01:48] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 11:01:48] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 11:01:48] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 11:01:48] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 11:01:48] Quantiles of plotted data range: 0.882790650772113,0.966942481185594,0.998792930197712,1.03387941341448,1.11821578824489
INFO [2021-03-11 11:01:49] plot_cnv_observations:Writing observation data to plot_out2/infercnv.preliminary.observations.txt
INFO [2021-03-11 11:01:49] plot_cnv_references:Start
INFO [2021-03-11 11:01:49] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 11:01:50] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 11:01:50] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 11:01:50] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 11:01:50] Quantiles of plotted data range: 0.882790650772113,0.978846385330733,0.998778646338114,1.02034944189329,1.11821578824489
INFO [2021-03-11 11:01:50] plot_cnv_references:Writing reference data to plot_out2/infercnv.preliminary.references.txt
INFO [2021-03-11 11:01:52]
STEP 17: HMM-based CNV prediction
INFO [2021-03-11 11:01:52] predict_CNV_via_HMM_on_whole_tumor_samples
INFO [2021-03-11 11:01:54] -done predicting CNV based on initial tumor subclusters
INFO [2021-03-11 11:01:55] get_predicted_CNV_regions(subcluster)
INFO [2021-03-11 11:01:55] -processing cell_group_name: epi.epi_s1, size: 57
INFO [2021-03-11 11:02:00] -processing cell_group_name: ref-fib.ref-fib_s1, size: 104
INFO [2021-03-11 11:02:04] -writing cell clusters file: plot_out2/17_HMM_predHMMi6.hmm_mode-samples.cell_groupings
INFO [2021-03-11 11:02:04] -writing cnv regions file: plot_out2/17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_regions.dat
INFO [2021-03-11 11:02:05] -writing per-gene cnv report: plot_out2/17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat
INFO [2021-03-11 11:02:05] -writing gene ordering info: plot_out2/17_HMM_predHMMi6.hmm_mode-samples.genes_used.dat
INFO [2021-03-11 11:02:06] ::plot_cnv:Start
INFO [2021-03-11 11:02:06] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=1360956 Min=1 Max=6.
INFO [2021-03-11 11:02:06] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 11:02:07] plot_cnv_observation:Start
INFO [2021-03-11 11:02:07] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 11:02:07] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 11:02:07] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 11:02:07] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 11:02:07] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 11:02:07] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 11:02:07] Quantiles of plotted data range: 1,3,3,4,6
INFO [2021-03-11 11:02:07] plot_cnv_observations:Writing observation data to plot_out2/infercnv.17_HMM_predHMMi6.hmm_mode-samples.observations.txt
INFO [2021-03-11 11:02:07] plot_cnv_references:Start
INFO [2021-03-11 11:02:07] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 11:02:08] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 11:02:08] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 11:02:08] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 11:02:08] Quantiles of plotted data range: 3,3,3,3,3
INFO [2021-03-11 11:02:08] plot_cnv_references:Writing reference data to plot_out2/infercnv.17_HMM_predHMMi6.hmm_mode-samples.references.txt
INFO [2021-03-11 11:02:09]
STEP 18: Run Bayesian Network Model on HMM predicted CNV's
INFO [2021-03-11 11:02:09] Creating the following Directory: plot_out2/BayesNetOutput.HMMi6.hmm_mode-samples
INFO [2021-03-11 11:02:09] Initializing new MCM InferCNV Object.
INFO [2021-03-11 11:02:09] validating infercnv_obj
INFO [2021-03-11 11:02:09] Total CNV's: 42
INFO [2021-03-11 11:02:09] Loading BUGS Model.
INFO [2021-03-11 11:02:09] Running Sampling Using Parallel with 4 Cores
Error in (function (srcref) : unimplemented type (29) in 'eval'
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error in FUN(X[[i]], ...) :
INTEGER() can only be applied to a 'integer', not a 'unknown type #29'
In addition: Warning message:
In FUN(X[[i]], ...) : type 29 is unimplemented in 'type2char'
同类问题
You might try updating Rstudio.