Error in bmRequest - Internal Server Error (HTTP 500)
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alexch.liu • 0
@alexchliu-22872
Last seen 5.5 years ago
Canada/Toronto/UniversityOfToronto

Hi,

I am using MAGeCKFlute to analyze my summary file from MAGeCK.

However, when I run

path.geneSummary <- "./Gr1PosvsGr1Neg.Ivo.gene_summary.txt"
path.sgRNASummary <- "./Gr1PosvsGr1Neg.Ivo.sgrna_summary.txt"

FluteRRA(gene_summary = path.geneSummary, 
                 sgrna_summary = path.sgRNASummary,
                 proj = "Apr08",
                 organism = "mmu"
                  )

It throws the error

Error in bmRequest(request = request, verbose = verbose) : 
  Internal Server Error (HTTP 500).

When I run the function EnrichAnalyzer, it also creates the same error.

enrich <- EnrichAnalyzer(genelist, method = "GSEA", type = "GOBP")
2020-04-08 20:15:27 # Running GOBP enrichment analysis
2020-Apr-08 8:15:27 PM Downloading genesets from Gene Ontology ...
Error in bmRequest(request = request, verbose = verbose) : 
  Internal Server Error (HTTP 500).



md5-6402c169a4e26d9f981ca377fced1997



sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252 
[2] LC_CTYPE=English_Canada.1252   
[3] LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
[6] methods   base     

other attached packages:
 [1] forcats_0.5.0     stringr_1.4.0     dplyr_0.8.5      
 [4] purrr_0.3.3       readr_1.3.1       tidyr_1.0.2      
 [7] tibble_2.1.3      ggplot2_3.3.0     tidyverse_1.3.0  
[10] MAGeCKFlute_1.6.3

loaded via a namespace (and not attached):
  [1] readxl_1.3.1           backports_1.1.5       
  [3] fastmatch_1.1-0        BiocFileCache_1.10.2  
  [5] plyr_1.8.6             igraph_1.2.4.2        
  [7] splines_3.6.2          BiocParallel_1.20.1   
  [9] pathview_1.26.0        sva_3.34.0            
 [11] urltools_1.7.3         digest_0.6.25         
 [13] GOSemSim_2.12.1        viridis_0.5.1         
 [15] GO.db_3.10.0           fansi_0.4.1           
 [17] magrittr_1.5           memoise_1.1.0         
 [19] limma_3.42.2           Biostrings_2.54.0     
 [21] annotate_1.64.0        graphlayouts_0.6.0    
 [23] modelr_0.1.6           matrixStats_0.56.0    
 [25] askpass_1.1            enrichplot_1.6.1      
 [27] prettyunits_1.1.1      colorspace_1.4-1      
 [29] rvest_0.3.5            blob_1.2.1            
 [31] rappdirs_0.3.1         ggrepel_0.8.2         
 [33] haven_2.2.0            xfun_0.12             
 [35] crayon_1.3.4           RCurl_1.98-1.1        
 [37] jsonlite_1.6.1         graph_1.64.0          
 [39] genefilter_1.68.0      survival_3.1-8        
 [41] glue_1.3.2             polyclip_1.10-0       
 [43] gtable_0.3.0           zlibbioc_1.32.0       
 [45] XVector_0.26.0         Rgraphviz_2.30.0      
 [47] BiocGenerics_0.32.0    scales_1.1.0          
 [49] DOSE_3.12.0            pheatmap_1.0.12       
 [51] DBI_1.1.0              Rcpp_1.0.4            
 [53] viridisLite_0.3.0      xtable_1.8-4          
 [55] progress_1.2.2         gridGraphics_0.5-0    
 [57] bit_1.1-15.2           europepmc_0.3         
 [59] stats4_3.6.2           httr_1.4.1            
 [61] fgsea_1.12.0           RColorBrewer_1.1-2    
 [63] pkgconfig_2.0.3        XML_3.99-0.3          
 [65] farver_2.0.3           dbplyr_1.4.2          
 [67] ggplotify_0.0.5        tidyselect_1.0.0      
 [69] labeling_0.3           rlang_0.4.5           
 [71] reshape2_1.4.3         AnnotationDbi_1.48.0  
 [73] munsell_0.5.0          cellranger_1.1.0      
 [75] tools_3.6.2            cli_2.0.2             
 [77] generics_0.0.2         RSQLite_2.2.0         
 [79] broom_0.5.5            ggridges_0.5.2        
 [81] yaml_2.2.1             fs_1.3.2              
 [83] knitr_1.28             bit64_0.9-7           
 [85] tidygraph_1.1.2        KEGGREST_1.26.1       
 [87] dendextend_1.13.4      ggraph_2.0.1          
 [89] nlme_3.1-142           KEGGgraph_1.46.0      
 [91] DO.db_2.9              xml2_1.2.5            
 [93] biomaRt_2.42.0         compiler_3.6.2        
 [95] rstudioapi_0.11        curl_4.3              
 [97] png_0.1-7              ggsignif_0.6.0        
 [99] reprex_0.3.0           tweenr_1.0.1          
[101] stringi_1.4.6          lattice_0.20-38       
[103] Matrix_1.2-18          ggsci_2.9             
[105] vctrs_0.2.4            pillar_1.4.3          
[107] lifecycle_0.2.0        BiocManager_1.30.10   
[109] triebeard_0.3.0        data.table_1.12.8     
[111] cowplot_1.0.0          bitops_1.0-6          
[113] qvalue_2.18.0          R6_2.4.1              
[115] gridExtra_2.3          IRanges_2.20.2        
[117] MASS_7.3-51.5          assertthat_0.2.1      
[119] openssl_1.4.1          withr_2.1.2           
[121] S4Vectors_0.24.3       mgcv_1.8-31           
[123] parallel_3.6.2         hms_0.5.3             
[125] clusterProfiler_3.14.3 grid_3.6.2            
[127] rvcheck_0.1.8          ggpubr_0.2.5          
[129] ggforce_0.3.1          Biobase_2.46.0        
[131] lubridate_1.7.4       
software error • 920 views
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