Yelab2020 / Cottrazm

Construct Tumor Transition Zone Microenvironment
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cannot open file 'infercnv.17_HMM_predHMMi6.rand_trees.hmm_mode-subclusters.observations_dendrogram.txt' #15

Open upohsdscz opened 3 months ago

upohsdscz commented 3 months ago

The file "infercnv.17_HMM_predHMMi6.rand_trees.hmm_mode-subclusters.observations_dendrogram.txt" disappeared, can you help me solve it? image

Jonyyqn commented 1 month 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
xzz-1995 commented 1 week ago

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.