Error in apply(cnv_means, 2, function(i) which(i == max(i))) : dim(X) must have a positive length Calls: <Anonymous> -> <Anonymous> -> reassignCNV -> reassignCNV -> apply Execution halted #676
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FuduanPeng
changed the title
colnames<-(*tmp*, value = cnv_regions) : attempt to set 'colnames' on an object with less than two dimensions Calls: <Anonymous> ... <Anonymous> -> removeCNV -> removeCNV -> colnames<- Execution halted
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A different error other than the one I reported previously at step 18. Does anyone can help? Thank you very much! The detail as below,
Attaching SeuratObject
Attaching sp
Warning message:
package ‘Seurat’ was built under R version 4.0.5
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
The following objects are masked from ‘package:base’:
Loading required package: viridisLite
Warning message:
package ‘viridisLite’ was built under R version 4.0.5
Warning message:
package ‘readxl’ was built under R version 4.0.5
Warning message:
package ‘ggsci’ was built under R version 4.0.5
Attaching package: ‘cowplot’
The following object is masked from ‘package:patchwork’:
Attaching package: ‘data.table’
The following objects are masked from ‘package:dplyr’:
Warning message:
package ‘data.table’ was built under R version 4.0.5
Warning messages:
1: multiple methods tables found for ‘aperm’
2: replacing previous import ‘BiocGenerics::aperm’ by ‘DelayedArray::aperm’ when loading ‘SummarizedExperiment’
Attaching package: ‘future’
The following object is masked from ‘package:infercnv’:
Warning message:
package ‘future’ was built under R version 4.0.5
multicore:
args: function (..., workers = 20, envir = parent.frame())
tweaked: TRUE
call: plan("multicore", workers = 20)
[1] "next"
Genome matrix has multiple modalities, returning a list of matrices for this genome
Genome matrix has multiple modalities, returning a list of matrices for this genome
Genome matrix has multiple modalities, returning a list of matrices for this genome
INFO [2024-09-15 23:50:28] Parsing gene order file: gene_annotation.txt
INFO [2024-09-15 23:50:28] Parsing cell annotations file: cell_annotation.txt
INFO [2024-09-15 23:50:28] ::order_reduce:Start.
INFO [2024-09-15 23:50:29] .order_reduce(): expr and order match.
INFO [2024-09-15 23:50:30] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 18060,20850 Total=141874973 Min=0 Max=2827.
INFO [2024-09-15 23:50:30] num genes removed taking into account provided gene ordering list: 743 = 4.1140642303433% removed.
INFO [2024-09-15 23:50:30] -filtering out cells < 100 or > Inf, removing 0 % of cells
INFO [2024-09-15 23:50:34] validating infercnv_obj
INFO [2024-09-15 23:50:34] ::process_data:Start
INFO [2024-09-15 23:50:34] Checking for saved results.
INFO [2024-09-15 23:50:34] Trying to reload from step 17
INFO [2024-09-15 23:50:41] Using backup HMM from step 17
INFO [2024-09-15 23:50:41] Trying to reload from step 15
INFO [2024-09-15 23:51:10] Using backup from step 15
INFO [2024-09-15 23:51:10]
STEP 1: incoming data
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:10]
INFO [2024-09-15 23:51:17]
INFO [2024-09-15 23:51:17] Initializing new MCM InferCNV Object.
INFO [2024-09-15 23:51:18] validating infercnv_obj
INFO [2024-09-15 23:51:18] Total CNV's: 1
INFO [2024-09-15 23:51:18] Loading BUGS Model.
INFO [2024-09-15 23:51:18] Running Sampling Using Parallel with 4 Cores
INFO [2024-09-16 00:31:36] Obtaining probabilities post-sampling
INFO [2024-09-16 00:32:21] Gibbs sampling time: 41.0515922546387 Minutes
INFO [2024-09-16 00:34:36] ::plot_cnv:Start
INFO [2024-09-16 00:34:36] ::plot_cnv:Current data dimensions (r,c)=10098,20850 Total=570872.78474036 Min=0 Max=0.393521906159861.
INFO [2024-09-16 00:34:38] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2024-09-16 00:34:42] plot_cnv_observation:Start
INFO [2024-09-16 00:34:42] Observation data size: Cells= 11699 Genes= 10098
INFO [2024-09-16 00:34:44] plot_cnv_observation:Writing observation groupings/color.
INFO [2024-09-16 00:34:44] plot_cnv_observation:Done writing observation groupings/color.
INFO [2024-09-16 00:34:44] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2024-09-16 00:34:44] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2024-09-16 00:35:02] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2024-09-16 00:35:02] Quantiles of plotted data range: 0,0,0,0,0.393521906159861
INFO [2024-09-16 00:35:14] plot_cnv_observations:Writing observation data to output_dir/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.observations.txt
INFO [2024-09-16 00:36:17] plot_cnv_references:Start
INFO [2024-09-16 00:36:17] Reference data size: Cells= 9151 Genes= 10098
INFO [2024-09-16 03:30:54] plot_cnv_references:Number reference groups= 1
INFO [2024-09-16 03:30:55] plot_cnv_references:Plotting heatmap.
INFO [2024-09-16 03:31:25] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2024-09-16 03:31:25] Quantiles of plotted data range: 0,0,0,0,0
INFO [2024-09-16 03:31:35] plot_cnv_references:Writing reference data to output_dir/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.references.txt
INFO [2024-09-16 03:35:01] Attempting to removing CNV(s) with a probability of being normal above 0.5
INFO [2024-09-16 03:35:01] Removing 1 CNV(s) identified by the HMM.
INFO [2024-09-16 03:35:02] Total CNV's after removing: 0
INFO [2024-09-16 03:35:02] Reassigning CNVs based on state probabilities.
Error in apply(cnv_means, 2, function(i) which(i == max(i))) :
dim(X) must have a positive length
Calls: -> -> reassignCNV -> reassignCNV -> apply
Execution halted
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.7 (Ootpa)
Matrix products: default
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] infercnv_1.6.0 data.table_1.14.2 cowplot_1.1.3
[4] ggsci_2.9 readxl_1.4.1 viridis_0.6.5
[7] viridisLite_0.4.1 dplyr_1.1.4 patchwork_1.2.0.9000
[10] ggplot2_3.5.1 sp_1.5-0 SeuratObject_4.1.1
[13] Seurat_4.1.1
loaded via a namespace (and not attached):
[1] plyr_1.8.7 igraph_2.0.3
[3] lazyeval_0.2.2 splines_4.0.3
[5] listenv_0.8.0 scattermore_0.8
[7] TH.data_1.1-2 GenomeInfoDb_1.26.4
[9] digest_0.6.36 foreach_1.5.2
[11] htmltools_0.5.8.1 fansi_1.0.3
[13] magrittr_2.0.3 tensor_1.5
[15] cluster_2.1.3 doParallel_1.0.17
[17] ROCR_1.0-11 limma_3.46.0
[19] fastcluster_1.2.6 globals_0.16.1
[21] matrixStats_0.62.0 sandwich_3.1-0
[23] spatstat.sparse_3.1-0 colorspace_2.0-3
[25] ggrepel_0.9.5 libcoin_1.0-10
[27] RCurl_1.98-1.3 jsonlite_1.8.8
[29] progressr_0.11.0 spatstat.data_3.1-2
[31] survival_3.4-0 zoo_1.8-11
[33] iterators_1.0.14 ape_5.8
[35] glue_1.6.2 polyclip_1.10-0
[37] gtable_0.3.1 zlibbioc_1.36.0
[39] XVector_0.30.0 leiden_0.4.3
[41] DelayedArray_0.16.3 future.apply_1.9.1
[43] SingleCellExperiment_1.12.0 BiocGenerics_0.50.0
[45] abind_1.4-5 scales_1.3.0
[47] mvtnorm_1.2-5 futile.options_1.0.1
[49] edgeR_4.2.0 miniUI_0.1.1.1
[51] Rcpp_1.0.9 xtable_1.8-4
[53] reticulate_1.30 spatstat.core_2.3-2
[55] stats4_4.0.3 htmlwidgets_1.5.4
[57] httr_1.4.7 gplots_3.1.3
[59] RColorBrewer_1.1-3 modeltools_0.2-23
[61] ica_1.0-3 reshape_0.8.9
[63] pkgconfig_2.0.3 uwot_0.1.14
[65] deldir_1.0-6 locfit_1.5-9.4
[67] utf8_1.2.2 tidyselect_1.2.1
[69] rlang_1.1.4 reshape2_1.4.4
[71] later_1.2.0 munsell_0.5.0
[73] cellranger_1.1.0 tools_4.0.3
[75] cli_3.6.3 generics_0.1.3
[77] ggridges_0.5.4 stringr_1.5.1
[79] fastmap_1.2.0 argparse_2.2.3
[81] goftest_1.2-3 fitdistrplus_1.1-8
[83] caTools_1.18.2 purrr_1.0.2
[85] RANN_2.6.1 coin_1.4-3
[87] pbapply_1.5-0 future_1.28.0
[89] nlme_3.1-159 mime_0.12
[91] formatR_1.12 compiler_4.0.3
[93] plotly_4.10.0 png_0.1-7
[95] spatstat.utils_3.0-5 tibble_3.2.1
[97] stringi_1.7.6 futile.logger_1.4.3
[99] rgeos_0.5-8 lattice_0.20-45
[101] Matrix_1.4-1 vctrs_0.6.5
[103] pillar_1.9.0 lifecycle_1.0.4
[105] spatstat.geom_3.2-9 lmtest_0.9-40
[107] RcppAnnoy_0.0.19 bitops_1.0-7
[109] irlba_2.3.5 httpuv_1.6.6
[111] GenomicRanges_1.42.0 R6_2.5.1
[113] promises_1.2.0.1 KernSmooth_2.23-20
[115] gridExtra_2.3 rjags_4-15
[117] IRanges_2.24.1 parallelly_1.32.1
[119] codetools_0.2-18 lambda.r_1.2.4
[121] gtools_3.9.3 MASS_7.3-58.1
[123] SummarizedExperiment_1.20.0 withr_2.5.0
[125] sctransform_0.3.4 multcomp_1.4-25
[127] S4Vectors_0.28.1 GenomeInfoDbData_1.2.4
[129] mgcv_1.8-40 parallel_4.0.3
[131] grid_4.0.3 rpart_4.1.16
[133] tidyr_1.3.1 coda_0.19-4.1
[135] MatrixGenerics_1.2.1 Rtsne_0.16
[137] Biobase_2.50.0 shiny_1.9.1
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