Error in rep(contig_name, contig_tbl[contig_name]) : invalid 'times' argument

[xoocharles]

Hi:

I am experiencing error of "invalid 'times' argument" at the step18 of Infercnv (Ver. 1.7.1). Do you know how to solve this issue?
Thanks a lot!

STEP 18: Run Bayesian Network Model on HMM predicted CNV's
INFO [2020-12-30 15:53:26] Initializing new MCM InferCNV Object.
INFO [2020-12-30 15:53:26] validating infercnv_obj
INFO [2020-12-30 15:53:27] Total CNV's: 131
INFO [2020-12-30 15:53:27] Loading BUGS Model.
INFO [2020-12-30 15:53:29] Running Sampling Using Parallel with 4 Cores
INFO [2020-12-31 11:24:33] Obtaining probabilities post-sampling
INFO [2020-12-31 13:08:38] Gibbs sampling time: 1275.15057635705 Minutes
INFO [2020-12-31 13:43:52] ::plot_cnv:Start
INFO [2020-12-31 13:43:52] ::plot_cnv:Current data dimensions (r,c)=9603,49805 Total=24344930.8598955 Min=0 Max=0.987066160772883.
INFO [2020-12-31 13:44:07] ::plot_cnv:Depending on the size of the matrix this may take a moment.
Error in rep(contig_name, contig_tbl[contig_name]) :
invalid 'times' argument

SessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2

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] Seurat_3.2.3 rjags_4-10 coda_0.19-4 infercnv_1.7.1

loaded via a namespace (and not attached):
[1] plyr_1.8.6 igraph_1.2.6
[3] lazyeval_0.2.2 splines_4.0.0
[5] listenv_0.8.0 scattermore_0.7
[7] GenomeInfoDb_1.26.2 ggplot2_3.3.2
[9] TH.data_1.0-10 digest_0.6.27
[11] foreach_1.5.1 htmltools_0.5.0
[13] fansi_0.4.1 magrittr_2.0.1
[15] tensor_1.5 cluster_2.1.0
[17] doParallel_1.0.16 ROCR_1.0-11
[19] remotes_2.2.0 limma_3.46.0
[21] globals_0.14.0 fastcluster_1.1.25
[23] matrixStats_0.57.0 sandwich_3.0-0
[25] prettyunits_1.1.1 colorspace_2.0-0
[27] ggrepel_0.9.0 dplyr_1.0.2
[29] callr_3.5.1 crayon_1.3.4
[31] RCurl_1.98-1.2 jsonlite_1.7.2
[33] libcoin_1.0-6 spatstat_1.64-1
[35] spatstat.data_1.7-0 survival_3.1-12
[37] zoo_1.8-8 iterators_1.0.13
[39] ape_5.4-1 glue_1.4.2
[41] polyclip_1.10-0 gtable_0.3.0
[43] zlibbioc_1.36.0 XVector_0.30.0
[45] leiden_0.3.6 DelayedArray_0.16.0
[47] pkgbuild_1.2.0 future.apply_1.6.0
[49] SingleCellExperiment_1.12.0 BiocGenerics_0.36.0
[51] abind_1.4-5 scales_1.1.1
[53] futile.options_1.0.1 mvtnorm_1.1-1
[55] edgeR_3.32.0 miniUI_0.1.1.1
[57] Rcpp_1.0.5 viridisLite_0.3.0
[59] xtable_1.8-4 reticulate_1.18
[61] rsvd_1.0.3 stats4_4.0.0
[63] htmlwidgets_1.5.3 httr_1.4.2
[65] gplots_3.1.1 RColorBrewer_1.1-2
[67] modeltools_0.2-23 ellipsis_0.3.1
[69] ica_1.0-2 pkgconfig_2.0.3
[71] reshape_0.8.8 uwot_0.1.10
[73] deldir_0.2-3 locfit_1.5-9.4
[75] tidyselect_1.1.0 rlang_0.4.9
[77] reshape2_1.4.4 later_1.1.0.1
[79] munsell_0.5.0 tools_4.0.0
[81] cli_2.2.0 generics_0.1.0
[83] ggridges_0.5.2 stringr_1.4.0
[85] fastmap_1.0.1 argparse_2.0.3
[87] goftest_1.2-2 processx_3.4.5
[89] fitdistrplus_1.1-3 caTools_1.18.0
[91] purrr_0.3.4 RANN_2.6.1
[93] coin_1.3-1 pbapply_1.4-3
[95] future_1.21.0 nlme_3.1-147
[97] mime_0.9 formatR_1.7
[99] compiler_4.0.0 curl_4.3
[101] plotly_4.9.2.2 png_0.1-7
[103] spatstat.utils_1.17-0 tibble_3.0.4
[105] stringi_1.5.3 ps_1.5.0
[107] futile.logger_1.4.3 lattice_0.20-41
[109] Matrix_1.2-18 vctrs_0.3.6
[111] pillar_1.4.7 lifecycle_0.2.0
[113] lmtest_0.9-38 RcppAnnoy_0.0.18
[115] data.table_1.13.4 cowplot_1.1.0
[117] bitops_1.0-6 irlba_2.3.3
[119] httpuv_1.5.4 patchwork_1.1.1
[121] GenomicRanges_1.42.0 R6_2.5.0
[123] promises_1.1.1 KernSmooth_2.23-16
[125] gridExtra_2.3 IRanges_2.24.1
[127] parallelly_1.22.0 codetools_0.2-16
[129] lambda.r_1.2.4 assertthat_0.2.1
[131] MASS_7.3-51.5 gtools_3.8.2
[133] SummarizedExperiment_1.20.0 rprojroot_2.0.2
[135] withr_2.3.0 sctransform_0.3.2
[137] multcomp_1.4-15 S4Vectors_0.28.1
[139] GenomeInfoDbData_1.2.4 mgcv_1.8-31
[141] parallel_4.0.0 grid_4.0.0
[143] rpart_4.1-15 tidyr_1.1.2
[145] MatrixGenerics_1.2.0 Rtsne_0.15
[147] Biobase_2.50.0 shiny_1.5.0

[xoocharles]

I found some genes in MCMC_infercnv_obj@gene_order having no annotations at all (showing NA) (also mentioned in #248 ). After I added the missing info and run plot_cnv on that file, the process could proceed and generate some txt files but not readable png. I will try other means as suggested in #231. My question now is since this MCMC_infercnv_obj is the last output, can I consider it as the final product and proceed downstream analysis? Am I missing some important step after step18? Thanks for the help!