Fragment file is not indexed

[SaharBJ]

I am trying to go through this tutorial: https://stuartlab.org/signac/articles/pbmc_multiomic. I want the processed object so that I can attempt this tutorial: https://stuartlab.org/signac/articles/integrate_atac. I downloaded the tutorial data directly from the links.

> # load the RNA and ATAC data
> counts <- Read10X_h5("pbmc_granulocyte_sorted_10k_filtered_feature_bc_matrix.h5")
Genome matrix has multiple modalities, returning a list of matrices for this genome
> fragpath <- "pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz"
> # get gene annotations for hg38
> annotation <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 33s
There were 24 warnings (use warnings() to see them)
> seqlevels(annotation) <- paste0('chr', seqlevels(annotation))
> 
> # create a Seurat object containing the RNA adata
> pbmc <- CreateSeuratObject(
+     counts = counts$`Gene Expression`,
+     assay = "RNA"
+ )
> 
> # create ATAC assay and add it to the object
> pbmc[["ATAC"]] <- CreateChromatinAssay(
+     counts = counts$Peaks,
+     sep = c(":", "-"),
+     fragments = fragpath,
+     annotation = annotation
+ )
Error in GetIndexFile(fragment = path, verbose = verbose) : 
  Fragment file is not indexed.

> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_South Africa.utf8 
[2] LC_CTYPE=English_South Africa.utf8   
[3] LC_MONETARY=English_South Africa.utf8
[4] LC_NUMERIC=C                         
[5] LC_TIME=English_South Africa.utf8    

time zone: Africa/Johannesburg
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils    
[6] datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [2] BSgenome_1.74.0                  
 [3] rtracklayer_1.66.0               
 [4] BiocIO_1.16.0                    
 [5] EnsDb.Hsapiens.v86_2.99.0        
 [6] presto_1.0.0                     
 [7] data.table_1.16.2                
 [8] Rcpp_1.0.13-1                    
 [9] callr_3.7.6                      
[10] ps_1.8.1                         
[11] desc_1.4.3                       
[12] plotly_4.10.4                    
[13] rstudioapi_0.17.1                
[14] AnnotationHub_3.14.0             
[15] BiocFileCache_2.14.0             
[16] dbplyr_2.5.0                     
[17] biovizBase_1.54.0                
[18] backports_1.5.0                  
[19] evaluate_1.0.1                   
[20] ensembldb_2.30.0                 
[21] AnnotationFilter_1.30.0          
[22] GenomicFeatures_1.58.0           
[23] AnnotationDbi_1.68.0             
[24] Biobase_2.66.0                   
[25] memoise_2.0.1                    
[26] hdf5r_1.3.11                     
[27] patchwork_1.3.0                  
[28] Signac_1.14.0                    
[29] Matrix_1.7-0                     
[30] forcats_1.0.0                    
[31] stringr_1.5.1                    
[32] dplyr_1.1.4                      
[33] purrr_1.0.2                      
[34] tidyr_1.3.1                      
[35] tibble_3.2.1                     
[36] ggplot2_3.5.1                    
[37] tidyverse_2.0.0                  
[38] readr_2.1.5                      
[39] lubridate_1.9.3                  
[40] tzdb_0.4.0                       
[41] Seurat_5.1.0                     
[42] SeuratObject_5.0.2               
[43] sp_2.1-4                         
[44] Rsamtools_2.20.0                 
[45] Biostrings_2.72.1                
[46] XVector_0.44.0                   
[47] GenomicRanges_1.56.2             
[48] GenomeInfoDb_1.40.1              
[49] IRanges_2.38.1                   
[50] S4Vectors_0.42.1                 
[51] BiocGenerics_0.52.0              

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.38.0        
  [2] matrixStats_1.4.1          
  [3] spatstat.sparse_3.1-0      
  [4] bitops_1.0-9               
  [5] httr_1.4.7                 
  [6] RColorBrewer_1.1-3         
  [7] tools_4.4.1                
  [8] sctransform_0.4.1          
  [9] utf8_1.2.4                 
 [10] R6_2.5.1                   
 [11] lazyeval_0.2.2             
 [12] uwot_0.2.2                 
 [13] withr_3.0.2                
 [14] gridExtra_2.3              
 [15] progressr_0.15.0           
 [16] cli_3.6.3                  
 [17] spatstat.explore_3.3-3     
 [18] fastDummies_1.7.4          
 [19] spatstat.data_3.1-4        
 [20] ggridges_0.5.6             
 [21] pbapply_1.7-2              
 [22] foreign_0.8-87             
 [23] dichromat_2.0-0.1          
 [24] parallelly_1.39.0          
 [25] RSQLite_2.3.8              
 [26] generics_0.1.3             
 [27] ica_1.0-3                  
 [28] spatstat.random_3.3-2      
 [29] fansi_1.0.6                
 [30] abind_1.4-8                
 [31] lifecycle_1.0.4            
 [32] yaml_2.3.10                
 [33] SummarizedExperiment_1.36.0
 [34] SparseArray_1.6.0          
 [35] Rtsne_0.17                 
 [36] grid_4.4.1                 
 [37] blob_1.2.4                 
 [38] promises_1.3.0             
 [39] crayon_1.5.3               
 [40] miniUI_0.1.1.1             
 [41] lattice_0.22-6             
 [42] cowplot_1.1.3              
 [43] KEGGREST_1.46.0            
 [44] pillar_1.9.0               
 [45] knitr_1.49                 
 [46] rjson_0.2.23               
 [47] future.apply_1.11.3        
 [48] codetools_0.2-20           
 [49] fastmatch_1.1-4            
 [50] leiden_0.4.3.1             
 [51] glue_1.8.0                 
 [52] spatstat.univar_3.0-1      
 [53] vctrs_0.6.5                
 [54] png_0.1-8                  
 [55] spam_2.11-0                
 [56] gtable_0.3.6               
 [57] cachem_1.1.0               
 [58] xfun_0.49                  
 [59] S4Arrays_1.6.0             
 [60] mime_0.12                  
 [61] survival_3.7-0             
 [62] RcppRoll_0.3.1             
 [63] fitdistrplus_1.2-1         
 [64] ROCR_1.0-11                
 [65] nlme_3.1-166               
 [66] bit64_4.5.2                
 [67] filelock_1.0.3             
 [68] RcppAnnoy_0.0.22           
 [69] irlba_2.3.5.1              
 [70] KernSmooth_2.23-24         
 [71] rpart_4.1.23               
 [72] colorspace_2.1-1           
 [73] DBI_1.2.3                  
 [74] Hmisc_5.2-0                
 [75] nnet_7.3-19                
 [76] tidyselect_1.2.1           
 [77] processx_3.8.4             
 [78] bit_4.5.0                  
 [79] compiler_4.4.1             
 [80] curl_6.0.1                 
 [81] htmlTable_2.4.3            
 [82] DelayedArray_0.32.0        
 [83] checkmate_2.3.2            
 [84] scales_1.3.0               
 [85] lmtest_0.9-40              
 [86] rappdirs_0.3.3             
 [87] digest_0.6.37              
 [88] goftest_1.2-3              
 [89] spatstat.utils_3.1-0       
 [90] rmarkdown_2.29             
 [91] htmltools_0.5.8.1          
 [92] pkgconfig_2.0.3            
 [93] base64enc_0.1-3            
 [94] MatrixGenerics_1.18.0      
 [95] fastmap_1.2.0              
 [96] rlang_1.1.4                
 [97] htmlwidgets_1.6.4          
 [98] UCSC.utils_1.2.0           
 [99] shiny_1.9.1                
[100] farver_2.1.2               
[101] zoo_1.8-12                 
[102] jsonlite_1.8.9             
[103] BiocParallel_1.38.0        
[104] VariantAnnotation_1.52.0   
[105] RCurl_1.98-1.16            
[106] magrittr_2.0.3             
[107] Formula_1.2-5              
[108] GenomeInfoDbData_1.2.13    
[109] dotCall64_1.2              
[110] munsell_0.5.1              
[111] reticulate_1.39.0          
[112] stringi_1.8.4              
[113] zlibbioc_1.50.0            
[114] MASS_7.3-61                
[115] plyr_1.8.9                 
[116] parallel_4.4.1             
[117] listenv_0.9.1              
[118] ggrepel_0.9.6              
[119] deldir_2.0-4               
[120] splines_4.4.1              
[121] tensor_1.5                 
[122] hms_1.1.3                  
[123] igraph_2.1.1               
[124] spatstat.geom_3.3-3        
[125] RcppHNSW_0.6.0             
[126] reshape2_1.4.4             
[127] BiocVersion_3.20.0         
[128] XML_3.99-0.17              
[129] BiocManager_1.30.25        
[130] httpuv_1.6.15              
[131] RANN_2.6.2                 
[132] polyclip_1.10-7            
[133] future_1.34.0              
[134] scattermore_1.2            
[135] xtable_1.8-4               
[136] restfulr_0.0.15            
[137] RSpectra_0.16-2            
[138] later_1.3.2                
[139] viridisLite_0.4.2          
[140] GenomicAlignments_1.42.0   
[141] cluster_2.1.6              
[142] timechange_0.3.0           
[143] globals_0.16.3       

[timoast]

Is there an index present for the fragment file? The error message tells you that it cannot be found