Open upohsdscz opened 3 months ago
I also get the same Error. Any solutions ?
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-conda-linux-gnu
Running under: CentOS Linux 7 (Core)
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
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] loupeR_1.1.2 Cottrazm_0.1.1 org.Hs.eg.db_3.19.1
[4] AnnotationDbi_1.66.0 Biobase_2.62.0 clusterProfiler_4.12.6
[7] tibble_3.2.1 ggrepel_0.9.6 Rfast_2.1.0
[10] RcppParallel_5.1.9 RcppZiggurat_0.1.6 Rcpp_1.0.13
[13] data.table_1.16.2 quadprog_1.5-8 cowplot_1.1.3
[16] scatterpie_0.2.4 openxlsx_4.2.7.1 reticulate_1.39.0
[19] assertthat_0.2.1 dendextend_1.18.1 phylogram_2.1.0
[22] infercnv_1.20.0 rtracklayer_1.64.0 GenomicRanges_1.56.2
[25] GenomeInfoDb_1.40.1 IRanges_2.38.1 S4Vectors_0.40.2
[28] readr_2.1.5 BiocGenerics_0.48.1 ggtree_3.12.0
[31] patchwork_1.3.0 RColorBrewer_1.1-3 stringr_1.5.1
[34] ggplot2_3.5.1 Matrix_1.7-0 dplyr_1.1.4
[37] magrittr_2.0.3 SeuratObject_4.1.4 Seurat_4.4.0
loaded via a namespace (and not attached):
[1] fs_1.6.4 matrixStats_1.4.1
[3] spatstat.sparse_3.1-0 bitops_1.0-9
[5] enrichplot_1.24.4 httr_1.4.7
[7] doParallel_1.0.17 tools_4.4.1
[9] sctransform_0.4.1 utf8_1.2.4
[11] R6_2.5.1 lazyeval_0.2.2
[13] uwot_0.2.2 withr_3.0.1
[15] sp_2.1-4 gridExtra_2.3
[17] parallelDist_0.2.6 progressr_0.14.0
[19] argparse_2.2.3 cli_3.6.3
[21] formatR_1.14 spatstat.explore_3.3-2
[23] sandwich_3.1-1 mvtnorm_1.3-1
[25] spatstat.data_3.1-2 ggridges_0.5.6
[27] pbapply_1.7-2 Rsamtools_2.20.0
[29] yulab.utils_0.1.7 gson_0.1.0
[31] R.utils_2.12.3 DOSE_3.30.5
[33] parallelly_1.38.0 limma_3.60.6
[35] RSQLite_2.3.7 generics_0.1.3
[37] gridGraphics_0.5-1 BiocIO_1.14.0
[39] gtools_3.9.5 ica_1.0-3
[41] spatstat.random_3.3-2 zip_2.3.1
[43] GO.db_3.19.1 futile.logger_1.4.3
[45] fansi_1.0.6 abind_1.4-8
[47] R.methodsS3_1.8.2 lifecycle_1.0.4
[49] multcomp_1.4-26 yaml_2.3.10
[51] edgeR_4.0.16 SummarizedExperiment_1.34.0
[53] qvalue_2.36.0 gplots_3.2.0
[55] SparseArray_1.4.8 Rtsne_0.17
[57] blob_1.2.4 grid_4.4.1
[59] promises_1.3.0 crayon_1.5.3
[61] miniUI_0.1.1.1 lattice_0.22-6
[63] KEGGREST_1.44.1 pillar_1.9.0
[65] fgsea_1.30.0 rjson_0.2.23
[67] future.apply_1.11.2 codetools_0.2-20
[69] fastmatch_1.1-4 leiden_0.4.3.1
[71] glue_1.8.0 ggfun_0.1.6
[73] spatstat.univar_3.0-1 vctrs_0.6.5
[75] png_0.1-8 treeio_1.28.0
[77] gtable_0.3.5 cachem_1.1.0
[79] S4Arrays_1.4.1 mime_0.12
[81] tidygraph_1.3.1 libcoin_1.0-10
[83] coda_0.19-4.1 survival_3.7-0
[85] SingleCellExperiment_1.26.0 iterators_1.0.14
[87] statmod_1.5.0 fitdistrplus_1.2-1
[89] TH.data_1.1-2 ROCR_1.0-11
[91] nlme_3.1-166 bit64_4.5.2
[93] RcppAnnoy_0.0.22 irlba_2.3.5.1
[95] KernSmooth_2.23-24 DBI_1.2.3
[97] colorspace_2.1-1 tidyselect_1.2.1
[99] bit_4.5.0 compiler_4.4.1
[101] curl_5.2.1 httr2_1.0.5
[103] hdf5r_1.3.11 DelayedArray_0.30.1
[105] plotly_4.10.4 shadowtext_0.1.4
[107] scales_1.3.0 caTools_1.18.3
[109] lmtest_0.9-40 rappdirs_0.3.3
[111] digest_0.6.37 goftest_1.2-3
[113] spatstat.utils_3.1-0 XVector_0.42.0
[115] htmltools_0.5.8.1 pkgconfig_2.0.3
[117] MatrixGenerics_1.14.0 fastmap_1.2.0
[119] rlang_1.1.4 htmlwidgets_1.6.4
[121] UCSC.utils_1.0.0 shiny_1.9.1
[123] farver_2.1.2 zoo_1.8-12
[125] jsonlite_1.8.9 BiocParallel_1.36.0
[127] R.oo_1.26.0 GOSemSim_2.30.2
[129] RCurl_1.98-1.16 modeltools_0.2-23
[131] GenomeInfoDbData_1.2.12 ggplotify_0.1.2
[133] munsell_0.5.1 ape_5.8
[135] viridis_0.6.5 stringi_1.8.4
[137] ggraph_2.2.1 zlibbioc_1.48.2
[139] MASS_7.3-61 plyr_1.8.9
[141] parallel_4.4.1 listenv_0.9.1
[143] deldir_2.0-4 graphlayouts_1.2.0
[145] Biostrings_2.72.1 splines_4.4.1
[147] tensor_1.5 hms_1.1.3
[149] locfit_1.5-9.10 igraph_2.0.3
[151] fastcluster_1.2.6 spatstat.geom_3.3-3
[153] reshape2_1.4.4 futile.options_1.0.1
[155] XML_3.99-0.17 lambda.r_1.2.4
[157] tzdb_0.4.0 phyclust_0.1-34
[159] foreach_1.5.2 tweenr_2.0.3
[161] httpuv_1.6.15 RANN_2.6.2
[163] tidyr_1.3.1 purrr_1.0.2
[165] polyclip_1.10-7 future_1.34.0
[167] scattermore_1.2 ggforce_0.4.2
[169] coin_1.4-3 xtable_1.8-4
[171] restfulr_0.0.15 tidytree_0.4.6
[173] later_1.3.2 viridisLite_0.4.2
[175] rjags_4-16 aplot_0.2.3
[177] memoise_2.0.1 GenomicAlignments_1.40.0
[179] cluster_2.1.6 globals_0.16.3
Hello, this error might be due to the version of infercnv you used. The version used in the package was 1.8.1, yours was 1.20.0. Or some parameters used when running infercnv. such as subcluster model. you can check the output files of step 17 when running infercnnv, if the parameter selection is correct, then it should be the version problem. Thank you.
The file "infercnv.17_HMM_predHMMi6.rand_trees.hmm_mode-subclusters.observations_dendrogram.txt" disappeared, can you help me solve it?