Error in FindIntegrationAnchors

[kryptonitecircuit2002]

Hello! I am trying to integrate ATAC assay of a multiome object but my FindIntegrationAnchors for ATAC assay keeps running into issues:

integration.anchors.atac.h2 <- FindIntegrationAnchors(object.list = list(Control_H2, H2), anchor.features = rownames(Control_H2), reduction = "rlsi", dims = 2:30)
Computing within dataset neighborhoods
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01s  
Finding all pairwise anchors
  |                                                  | 0 % ~calculating  
Converting layer counts in assay ATAC to empty dgCMatrix
Error: unable to find an inherited method for function 'seqinfo' for signature 'x = "ChromatinAssay"'

I am confused because it worked when I ran it for other objects couple of months ago. Kindly look into it and let me know of the issue.

[timoast]

Hi, please include your full code and the output of sessionInfo()

[kryptonitecircuit2002]

This is the script I am trying to run:

lapply(required_packages, library, character.only = TRUE)
set.seed(1234)

#Normalize ATAC assay
DefaultAssay(H2.combined) <- "ATAC"
H2.combined <- RunTFIDF(H2.combined)
H2.combined <- FindTopFeatures(H2.combined, min.cutoff = 'q5')
H2.combined <- RunSVD(H2.combined)

# Cluster and visualize ATAC-seq data
H2.combined <- FindNeighbors(H2.combined, reduction = "lsi", dims = 2:30)
H2.combined <- FindClusters(H2.combined, resolution = 0.5)
H2.combined <- RunUMAP(H2.combined, dims = 2:30, reduction = "lsi", spread = 0.15, min.dist = 0.25, reduction.name = "umap.atac.h2")
DimPlot(H2.combined, reduction = "umap.atac.h2", label = TRUE, label.size = 4, repel = TRUE, split.by = "orig.ident") + ggtitle("ATAC UMAP")

# Integrate ATAC data
DefaultAssay(Control_H2) <- "ATAC"
Control_H2 <- RunTFIDF(Control_H2)
Control_H2 <- FindTopFeatures(Control_H2, min.cutoff = 'q0')
Control_H2 <- RunSVD(Control_H2, reduction.name = "lsi")

DefaultAssay(H2) <- "ATAC"
H2 <- RunTFIDF(H2)
H2 <- FindTopFeatures(H2, min.cutoff = 'q0')
H2 <- RunSVD(H2, reduction.name = "lsi")

#Integrate
integration.anchors.atac.h2 <- FindIntegrationAnchors(object.list = list(Control_H2, H2), anchor.features = rownames(Control_H2), reduction = "rlsi", dims = 2:30)
H2_integrated <- IntegrateEmbeddings(anchorset = integration.anchors.atac.h2, reductions = H2.combined.sct[["lsi"]], new.reduction.name = "integrated_lsi", dims.to.integrate = 2:30)
H2.combined.sct[['integrated_lsi_atac']] <- CreateDimReducObject(Embeddings(H3_integrated, "integrated_lsi")[colnames(H3.combined.sct),], key = "INTEGRATEDLSIATAC_", assay = "peaks")
H2.combined.sct <- FindNeighbors(H2.combined.sct, reduction = "integrated_lsi_atac", dims = 2:29)
H2.combined.sct <- FindClusters(H2.combined.sct, resolution = 0.5)
H2.combined.sct <- RunUMAP(H2.combined.sct, dims = 2:29, reduction = "integrated_lsi_atac", spread = 0.7, min.dist = 0.3, reduction.name = "umap.atac.int.h3")
DimPlot(H2.combined.sct, reduction = "umap.atac.int.h2", label = TRUE, label.size = 4, repel = TRUE, split.by = "orig.ident") + ggtitle("ATAC UMAP")

Here is the sessioninfo:

sessionInfo()
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=English_India.utf8  LC_CTYPE=English_India.utf8    LC_MONETARY=English_India.utf8
[4] LC_NUMERIC=C                   LC_TIME=English_India.utf8    

time zone: Asia/Calcutta
tzcode source: internal

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

other attached packages:
 [1] rtracklayer_1.68.0      ensembldb_2.32.0        AnnotationFilter_1.32.0 GenomicFeatures_1.60.0 
 [5] AnnotationDbi_1.70.0    Biobase_2.68.0          MASS_7.3-65             LSD_4.1-0              
 [9] ggrepel_0.9.6           pheatmap_1.0.13         readr_2.2.0             hdf5r_1.3.12           
[13] patchwork_1.3.2         future_1.70.0           GenomicRanges_1.60.0    GenomeInfoDb_1.44.3    
[17] IRanges_2.42.0          S4Vectors_0.46.0        BiocGenerics_0.54.1     generics_0.1.4         
[21] ggplot2_4.0.2           dplyr_1.1.4             Signac_1.17.1           Seurat_5.4.0           
[25] SeuratObject_5.3.0      sp_2.2-0               

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.40.0                     fs_1.6.6                               
  [3] matrixStats_1.5.0                       spatstat.sparse_3.1-0                  
  [5] bitops_1.0-9                            enrichplot_1.28.4                      
  [7] DirichletMultinomial_1.50.0             TFBSTools_1.46.0                       
  [9] httr_1.4.8                              RColorBrewer_1.1-3                     
 [11] doParallel_1.0.17                       tools_4.5.1                            
 [13] sctransform_0.4.3                       R6_2.6.1                               
 [15] lazyeval_0.2.2                          uwot_0.2.4                             
 [17] GetoptLong_1.1.1                        withr_3.0.2                            
 [19] gridExtra_2.3                           progressr_0.19.0                       
 [21] cli_3.6.5                               spatstat.explore_3.7-0                 
 [23] fastDummies_1.7.6                       labeling_0.4.3                         
 [25] S7_0.2.1                                spatstat.data_3.1-9                    
 [27] ggridges_0.5.7                          pbapply_1.7-4                          
 [29] Rsamtools_2.24.0                        yulab.utils_0.2.4                      
 [31] DOSE_4.2.0                              R.utils_2.13.0                         
 [33] dichromat_2.0-0.1                       parallelly_1.46.1                      
 [35] plotrix_3.8-14                          BSgenome_1.76.0                        
 [37] rstudioapi_0.18.0                       RSQLite_2.4.5                          
 [39] gridGraphics_0.5-1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [41] shape_1.4.6.1                           BiocIO_1.18.0                          
 [43] gtools_3.9.5                            ica_1.0-3                              
 [45] spatstat.random_3.4-4                   GO.db_3.21.0                           
 [47] Matrix_1.7-3                            abind_1.4-8                            
 [49] R.methodsS3_1.8.2                       lifecycle_1.0.5                        
 [51] yaml_2.3.12                             SummarizedExperiment_1.38.1            
 [53] gplots_3.3.0                            qvalue_2.40.0                          
 [55] SparseArray_1.8.1                       Rtsne_0.17                             
 [57] grid_4.5.1                              blob_1.3.0                             
 [59] promises_1.5.0                          pwalign_1.4.0                          
 [61] crayon_1.5.3                            miniUI_0.1.2                           
 [63] ggtangle_0.1.2                          lattice_0.22-7                         
 [65] cowplot_1.2.0                           KEGGREST_1.48.1                        
 [67] pillar_1.11.1                           ComplexHeatmap_2.24.1                  
 [69] fgsea_1.34.2                            rjson_0.2.23                           
 [71] boot_1.3-31                             future.apply_1.20.2                    
 [73] codetools_0.2-20                        fastmatch_1.1-8                        
 [75] glue_1.8.0                              ggfun_0.2.0                            
 [77] spatstat.univar_3.1-6                   data.table_1.18.0                      
 [79] vctrs_0.7.1                             png_0.1-8                              
 [81] treeio_1.32.0                           spam_2.11-3                            
 [83] gtable_0.3.6                            cachem_1.1.0                           
 [85] S4Arrays_1.8.1                          mime_0.13                              
 [87] survival_3.8-3                          RcppRoll_0.3.2                         
 [89] iterators_1.0.14                        fitdistrplus_1.2-6                     
 [91] ROCR_1.0-12                             nlme_3.1-168                           
 [93] ggtree_3.16.3                           bit64_4.6.0-1                          
 [95] RcppAnnoy_0.0.23                        irlba_2.3.5.1                          
 [97] KernSmooth_2.23-26                      otel_0.2.0                             
 [99] colorspace_2.1-2                        seqLogo_1.74.0                         
[101] DBI_1.3.0                               tidyselect_1.2.1                       
[103] bit_4.6.0                               compiler_4.5.1                         
[105] curl_7.1.0                              DelayedArray_0.34.1                    
[107] plotly_4.12.0                           scales_1.4.0                           
[109] caTools_1.18.3                          lmtest_0.9-40                          
[111] ChIPseeker_1.44.0                       rappdirs_0.3.4                         
[113] stringr_1.6.0                           digest_0.6.39                          
[115] goftest_1.2-3                           spatstat.utils_3.2-1                   
[117] XVector_0.48.0                          htmltools_0.5.9                        
[119] pkgconfig_2.0.3                         sparseMatrixStats_1.20.0               
[121] MatrixGenerics_1.20.0                   fastmap_1.2.0                          
[123] rlang_1.1.7                             GlobalOptions_0.1.4                    
[125] htmlwidgets_1.6.4                       UCSC.utils_1.4.0                       
[127] shiny_1.13.0                            farver_2.1.2                           
[129] zoo_1.8-15                              jsonlite_2.0.0                         
[131] BiocParallel_1.42.1                     GOSemSim_2.34.0                        
[133] R.oo_1.27.1                             RCurl_1.98-1.18                        
[135] magrittr_2.0.4                          GenomeInfoDbData_1.2.14                
[137] ggplotify_0.1.3                         dotCall64_1.2                          
[139] Rcpp_1.1.1                              ape_5.8-1                              
[141] reticulate_1.44.1                       stringi_1.8.7                          
[143] plyr_1.8.9                              parallel_4.5.1                         
[145] listenv_0.10.1                          deldir_2.0-4                           
[147] Biostrings_2.76.0                       splines_4.5.1                          
[149] tensor_1.5.1                            hms_1.1.4                              
[151] circlize_0.4.18                         igraph_2.3.1                           
[153] spatstat.geom_3.7-0                     RcppHNSW_0.6.0                         
[155] reshape2_1.4.5                          TFMPvalue_1.0.0                        
[157] XML_3.99-0.23                           tzdb_0.5.0                             
[159] foreach_1.5.2                           httpuv_1.6.16                          
[161] RANN_2.6.2                              tidyr_1.3.2                            
[163] purrr_1.2.1                             polyclip_1.10-7                        
[165] clue_0.3-68                             scattermore_1.2                        
[167] xtable_1.8-8                            restfulr_0.0.16                        
[169] RSpectra_0.16-2                         tidytree_0.4.7                         
[171] later_1.4.5                             viridisLite_0.4.3                      
[173] tibble_3.3.1                            aplot_0.2.9                            
[175] memoise_2.0.1                           GenomicAlignments_1.44.0               
[177] cluster_2.1.8.1                         globals_0.19.1

[timoast]

Try re-installing Bioconductor and Signac and restarting R

[timoast]

Closing as I haven't heard back, please re-open if you're still having issues