error during addGeneIntegrationMatrix with Seurat object

[kinako0130]

I wanted to do addGeneIntegrationMatrix command with Seurat object, but the error happened.

(My scATAC ArchR object and scRNA Seurat object is not paired. It's not the problem, right?)

projHeme2 <- addGeneIntegrationMatrix(
+ ArchRProj = projHeme2,
+ useMatrix = "GeneScoreMatrix",
+ matrixName = "GeneIntegrationMatrix",
+ reducedDims = "IterativeLSI",
+ seRNA =data,
+ addToArrow = TRUE,
+ force= TRUE,
+ groupRNA = "orig.ident",
+ nameCell = "predictedCell",
+ nameGroup = "predictedGroup",
+ nameScore = "predictedScore",
+ reduction = "cca"
+ )

output is this

ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-e718351806e0-Date-2023-11-01_Time-14-47-10.075343.log
If there is an issue, please report to github with logFile!
2023-11-01 14:47:14.401067 : Running Seurat's Integration Stuart* et al 2019, 0.072 mins elapsed.
2023-11-01 14:47:14.503903 : Checking ATAC Input, 0.074 mins elapsed.
2023-11-01 14:47:18.31113 : Checking RNA Input, 0.137 mins elapsed.
2023-11-01 14:47:26.504353 : Found 17493 overlapping gene names from gene scores and rna matrix!, 0.274 mins elapsed.
2023-11-01 14:47:26.510016 : Creating Integration Blocks, 0.274 mins elapsed.
2023-11-01 14:47:26.587384 : Prepping Interation Data, 0.275 mins elapsed.
2023-11-01 14:47:27.063394 : Computing Integration in 1 Integration Blocks!, 0 mins elapsed.
2023-11-01 14:47:27.067481 : Block (1 of 1) : Computing Integration, 0 mins elapsed.
2023-11-01 14:47:31.901341 : Block (1 of 1) : Identifying Variable Genes, 0.081 mins elapsed.
2023-11-01 14:47:37.921137 : Block (1 of 1) : Getting GeneScoreMatrix, 0.181 mins elapsed.
2023-11-01 14:47:44.683539 : Block (1 of 1) : Imputing GeneScoreMatrix, 0.294 mins elapsed.
Getting ImputeWeights
2023-11-01 14:48:00.240479 : Block (1 of 1) : Seurat FindTransferAnchors, 0.553 mins elapsed.
<simpleError in dimnames(x) <- dn: length of 'dimnames' [1] not equal to array extent>
Error in .retryCatch({ : 

This is my Seurat object.

> str(data)
Formal class 'Seurat' [package "Seurat"] with 13 slots
  ..@ assays      :List of 1
  .. ..$ RNA:Formal class 'Assay' [package "Seurat"] with 8 slots
  .. .. .. ..@ counts       :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. .. .. ..@ i       : int [1:124973672] 2 3 5 6 9 10 11 13 14 23 ...
  .. .. .. .. .. ..@ p       : int [1:14250] 0 9029 19236 29814 38296 46993 55983 67560 78372 87989 ...
  .. .. .. .. .. ..@ Dim     : int [1:2] 34617 14249
  .. .. .. .. .. ..@ Dimnames:List of 2
  .. .. .. .. .. .. ..$ : chr [1:34617] "0610005C13Rik" "0610006L08Rik" "0610007P14Rik" "0610009B22Rik" ...
  .. .. .. .. .. .. ..$ : chr [1:14249] "F1S4_160108_001_A01" "F1S4_160108_001_B01" "F1S4_160108_001_C01" "F1S4_160108_001_D01" ...
  .. .. .. .. .. ..@ x       : num [1:124973672] 79 140 29 48 30 114 575 7 108 206 ...
  .. .. .. .. .. ..@ factors : list()
  .. .. .. ..@ data         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. .. .. ..@ i       : int [1:124973672] 2 3 5 6 9 10 11 13 14 23 ...
  .. .. .. .. .. ..@ p       : int [1:14250] 0 9029 19236 29814 38296 46993 55983 67560 78372 87989 ...
  .. .. .. .. .. ..@ Dim     : int [1:2] 34617 14249
  .. .. .. .. .. ..@ Dimnames:List of 2
  .. .. .. .. .. .. ..$ : chr [1:34617] "0610005C13Rik" "0610006L08Rik" "0610007P14Rik" "0610009B22Rik" ...
  .. .. .. .. .. .. ..$ : chr [1:14249] "F1S4_160108_001_A01" "F1S4_160108_001_B01" "F1S4_160108_001_C01" "F1S4_160108_001_D01" ...
  .. .. .. .. .. ..@ x       : num [1:124973672] 79 140 29 48 30 114 575 7 108 206 ...
  .. .. .. .. .. ..@ factors : list()
  .. .. .. ..@ scale.data   : num[0 , 0 ] 
  .. .. .. ..@ assay.orig   : NULL
  .. .. .. ..@ var.features : logi(0) 
  .. .. .. ..@ meta.features:'data.frame':      34617 obs. of  0 variables
  .. .. .. ..@ misc         : NULL
  .. .. .. ..@ key          : chr "rna_"
  ..@ meta.data   :'data.frame':        14249 obs. of  52 variables:
  .. ..$ orig.ident                   : Factor w/ 3 levels "F1S4","F2S4",..: 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ nCount_RNA                   : num [1:14249] 1730700 1909605 1984948 2291552 1757463 ...
  .. ..$ nFeature_RNA                 : int [1:14249] 9029 10207 10578 8482 8697 8990 11577 10812 9617 9037 ...
  .. ..$ sample_id                    : int [1:14249] 527128530 527128536 527128542 527128548 527128554 527128560 527128566 527128572 527128578 527128584 ...
  .. ..$ sample_type                  : chr [1:14249] "Cells" "Cells" "Cells" "Cells" ...
  .. ..$ organism                     : chr [1:14249] "Mus musculus" "Mus musculus" "Mus musculus" "Mus musculus" ...
  .. ..$ donor                        : int [1:14249] 225675 225675 225675 225675 225675 225675 225675 225675 225675 225675 ...
  .. ..$ sex                          : chr [1:14249] "M" "M" "M" "M" ...
  .. ..$ age_days                     : int [1:14249] 53 53 53 53 53 53 53 53 53 53 ...
  .. ..$ eye_condition                : chr [1:14249] "Normal" "Normal" "Normal" "Normal" ...
  .. ..$ genotype                     : chr [1:14249] "Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt" "Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt" "Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt" "Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt" ...
  .. ..$ driver_lines                 : chr [1:14249] "Slc32a1-IRES-Cre" "Slc32a1-IRES-Cre" "Slc32a1-IRES-Cre" "Slc32a1-IRES-Cre" ...
  .. ..$ reporter_lines               : chr [1:14249] "Ai14(RCL-tdT)" "Ai14(RCL-tdT)" "Ai14(RCL-tdT)" "Ai14(RCL-tdT)" ...
  .. ..$ brain_hemisphere             : chr [1:14249] "L" "L" "L" "L" ...
  .. ..$ brain_region                 : chr [1:14249] "VISp" "VISp" "VISp" "VISp" ...
  .. ..$ brain_subregion              : chr [1:14249] "L2/3" "L2/3" "L2/3" "L2/3" ...
  .. ..$ injection_label_direction    : chr [1:14249] "No Injection" "No Injection" "No Injection" "No Injection" ...
  .. ..$ injection_primary            : chr [1:14249] "No Injection" "No Injection" "No Injection" "No Injection" ...
  .. ..$ injection_secondary          : chr [1:14249] "No Injection" "No Injection" "No Injection" "No Injection" ...
  .. ..$ injection_tract              : chr [1:14249] "No Injection" "No Injection" "No Injection" "No Injection" ...
  .. ..$ injection_material           : chr [1:14249] "No Injection" "No Injection" "No Injection" "No Injection" ...
  .. ..$ injection_exclusion_criterion: chr [1:14249] "No Injection" "No Injection" "No Injection" "No Injection" ...
  .. ..$ facs_date                    : chr [1:14249] "1/8/2016" "1/8/2016" "1/8/2016" "1/8/2016" ...
  .. ..$ facs_container               : chr [1:14249] "F1S4_160108_001" "F1S4_160108_001" "F1S4_160108_001" "F1S4_160108_001" ...
  .. ..$ facs_sort_criteria           : chr [1:14249] "RFP-positive" "RFP-positive" "RFP-positive" "RFP-positive" ...
  .. ..$ rna_amplification_set        : chr [1:14249] "A8S4_160202_01" "A8S4_160202_01" "A8S4_160202_01" "A8S4_160202_01" ...
  .. ..$ library_prep_set             : chr [1:14249] "L8S4_160205_01_A02" "L8S4_160205_01_B02" "L8S4_160205_01_C02" "L8S4_160205_01_D02" ...
  .. ..$ library_prep_avg_size_bp     : int [1:14249] 436 445 441 489 424 432 430 476 513 466 ...
  .. ..$ seq_name                     : chr [1:14249] "LS-15006_S09_E1-50" "LS-15006_S10_E1-50" "LS-15006_S11_E1-50" "LS-15006_S12_E1-50" ...
  .. ..$ seq_tube                     : chr [1:14249] "LS-15006" "LS-15006" "LS-15006" "LS-15006" ...
  .. ..$ seq_batch                    : chr [1:14249] "R8S4-160225" "R8S4-160225" "R8S4-160225" "R8S4-160225" ...
  .. ..$ total_reads                  : int [1:14249] 2865074 2986823 2881912 3094715 2626809 3074500 2837350 2476139 2170131 2812365 ...
  .. ..$ percent_exon_reads           : num [1:14249] 74.2 77.6 83.1 89.3 84.2 ...
  .. ..$ percent_intron_reads         : num [1:14249] 20.92 17.38 12.61 7.62 11.34 ...
  .. ..$ percent_intergenic_reads     : num [1:14249] 4.91 5.06 4.25 3.05 4.43 ...
  .. ..$ percent_rrna_reads           : num [1:14249] 0.136 0.117 0.116 0.257 0.16 ...
  .. ..$ percent_mt_exon_reads        : num [1:14249] 0.000105 0.000402 0.000312 0.000226 0.000381 ...
  .. ..$ percent_reads_unique         : num [1:14249] 83.8 84.3 84.3 84 80.9 ...
  .. ..$ percent_synth_reads          : num [1:14249] 0.00489 0.0039 0.00332 0.0058 0.00592 ...
  .. ..$ percent_ecoli_reads          : num [1:14249] 0.0196 0.0147 0.0127 0.0181 0.0306 ...
  .. ..$ percent_aligned_reads_total  : num [1:14249] 100 100 100 100 100 ...
  .. ..$ complexity_cg                : num [1:14249] 0.355 0.351 0.361 0.369 0.379 ...
  .. ..$ genes_detected_cpm_criterion : int [1:14249] 10445 11600 11848 9494 10012 10696 12692 11755 10680 10420 ...
  .. ..$ genes_detected_fpkm_criterion: int [1:14249] 9222 10370 10734 8561 8791 9145 11724 10939 9799 9197 ...
  .. ..$ tdt_cpm                      : num [1:14249] 249 290 281 390 254 ...
  .. ..$ gfp_cpm                      : num [1:14249] 249 290 281 390 254 ...
  .. ..$ class                        : chr [1:14249] "GABAergic" "GABAergic" "GABAergic" "GABAergic" ...
  .. ..$ subclass                     : chr [1:14249] "Vip" "Lamp5" "Lamp5" "Vip" ...
  .. ..$ cluster                      : chr [1:14249] "Vip Arhgap36 Hmcn1" "Lamp5 Lsp1" "Lamp5 Lsp1" "Vip Crispld2 Htr2c" ...
  .. ..$ confusion_score              : num [1:14249] 0.4385 0.1025 0.0195 0.2734 0.7532 ...
  .. ..$ cluster_correlation          : num [1:14249] 0.837 0.879 0.887 0.844 0.855 ...
  .. ..$ core_intermediate_call       : chr [1:14249] "Intermediate" "Core" "Core" "Core" ...
  ..@ active.assay: chr "RNA"
  ..@ active.ident: Factor w/ 3 levels "F1S4","F2S4",..: 1 1 1 1 1 1 1 1 1 1 ...
  .. ..- attr(*, "names")= chr [1:14249] "F1S4_160108_001_A01" "F1S4_160108_001_B01" "F1S4_160108_001_C01" "F1S4_160108_001_D01" ...
  ..@ graphs      : list()
  ..@ neighbors   : list()
  ..@ reductions  : list()
  ..@ images      : list()
  ..@ project.name: chr "SeuratProject"
  ..@ misc        : list()
  ..@ version     :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. ..$ : int [1:4] 3 1 1 9023
  ..@ commands    : list()
  ..@ tools       : list()

Could you teach my how to treat this error?

Also, these are my sessionInfo and log file
ArchR-addGeneIntegrationMatrix-e718351806e0-Date-2023-11-01_Time-14-47-10.075343.log

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /usr/lib64/libblas.so.3.4.2 
LAPACK: /usr/lib64/liblapack.so.3.4.2

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
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/Tokyo
tzcode source: system (glibc)

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

other attached packages:
 [1] scRNAseq_2.14.0                   ggrepel_0.9.4                    
 [3] hexbin_1.28.3                     circlize_0.4.15                  
 [5] ComplexHeatmap_2.16.0             Rtsne_0.16                       
 [7] pheatmap_1.0.12                   igraph_1.5.1                     
 [9] scran_1.28.2                      scuttle_1.10.3                   
[11] SingleCellExperiment_1.22.0       harmony_1.1.0                    
[13] uwot_0.1.16                       ggridges_0.5.4                   
[15] nabor_0.5.0                       SeuratObject_5.0.0               
[17] Seurat_4.4.0                      Rsamtools_2.16.0                 
[19] BSgenome.Mmusculus.UCSC.mm9_1.4.0 BSgenome_1.68.0                  
[21] rtracklayer_1.60.1                Biostrings_2.68.1                
[23] XVector_0.40.0                    rhdf5_2.44.0                     
[25] SummarizedExperiment_1.30.2       Biobase_2.60.0                   
[27] MatrixGenerics_1.12.3             Rcpp_1.0.11                      
[29] Matrix_1.6-1.1                    GenomicRanges_1.52.1             
[31] GenomeInfoDb_1.36.4               IRanges_2.34.1                   
[33] S4Vectors_0.38.2                  BiocGenerics_0.46.0              
[35] matrixStats_1.0.0                 data.table_1.14.8                
[37] stringr_1.5.0                     plyr_1.8.9                       
[39] magrittr_2.0.3                    ggplot2_3.4.4                    
[41] gtable_0.3.4                      gtools_3.9.4                     
[43] gridExtra_2.3                     ArchR_1.0.2                      

loaded via a namespace (and not attached):
  [1] fs_1.6.3                      ProtGenerics_1.32.0          
  [3] spatstat.sparse_3.0-3         bitops_1.0-7                 
  [5] devtools_2.4.5                httr_1.4.7                   
  [7] RColorBrewer_1.1-3            doParallel_1.0.17            
  [9] profvis_0.3.8                 tools_4.3.0                  
 [11] sctransform_0.4.1             utf8_1.2.4                   
 [13] R6_2.5.1                      lazyeval_0.2.2               
 [15] rhdf5filters_1.12.1           GetoptLong_1.0.5             
 [17] urlchecker_1.0.1              withr_2.5.2                  
 [19] sp_2.1-1                      prettyunits_1.2.0            
 [21] progressr_0.14.0              textshaping_0.3.7            
 [23] cli_3.6.1                     Cairo_1.6-1                  
 [25] spatstat.explore_3.2-5        labeling_0.4.3               
 [27] spatstat.data_3.0-3           pbapply_1.7-2                
 [29] systemfonts_1.0.5             sessioninfo_1.2.2            
 [31] parallelly_1.36.0             limma_3.56.2                 
 [33] RSQLite_2.3.2                 generics_0.1.3               
 [35] shape_1.4.6                   BiocIO_1.10.0                
 [37] ica_1.0-3                     spatstat.random_3.2-1        
 [39] dplyr_1.1.3                   fansi_1.0.5                  
 [41] abind_1.4-5                   lifecycle_1.0.3              
 [43] yaml_2.3.7                    edgeR_3.42.4                 
 [45] BiocFileCache_2.8.0           blob_1.2.4                   
 [47] promises_1.2.1                dqrng_0.3.1                  
 [49] ExperimentHub_2.8.1           crayon_1.5.2                 
 [51] miniUI_0.1.1.1                lattice_0.22-5               
 [53] beachmat_2.16.0               cowplot_1.1.1                
 [55] GenomicFeatures_1.52.2        KEGGREST_1.40.1              
 [57] pillar_1.9.0                  metapod_1.8.0                
 [59] rjson_0.2.21                  future.apply_1.11.0          
 [61] codetools_0.2-19              leiden_0.4.3                 
 [63] glue_1.6.2                    remotes_2.4.2.1              
 [65] vctrs_0.6.4                   png_0.1-8                    
 [67] spam_2.10-0                   cachem_1.0.8                 
 [69] S4Arrays_1.0.6                mime_0.12                    
 [71] survival_3.5-7                iterators_1.0.14             
 [73] statmod_1.5.0                 bluster_1.10.0               
 [75] interactiveDisplayBase_1.38.0 ellipsis_0.3.2               
 [77] fitdistrplus_1.1-11           ROCR_1.0-11                  
 [79] nlme_3.1-163                  usethis_2.2.2                
 [81] bit64_4.0.5                   progress_1.2.2               
 [83] filelock_1.0.2                RcppAnnoy_0.0.21             
 [85] rprojroot_2.0.3               irlba_2.3.5.1                
 [87] KernSmooth_2.23-22            colorspace_2.1-0             
 [89] DBI_1.1.3                     processx_3.8.2               
 [91] tidyselect_1.2.0              curl_5.1.0                   
 [93] bit_4.0.5                     compiler_4.3.0               
 [95] BiocNeighbors_1.18.0          xml2_1.3.5                   
 [97] desc_1.4.2                    DelayedArray_0.26.7          
 [99] plotly_4.10.3                 scales_1.2.1                 
[101] lmtest_0.9-40                 callr_3.7.3                  
[103] rappdirs_0.3.3                digest_0.6.33                
[105] goftest_1.2-3                 spatstat.utils_3.0-4         
[107] RhpcBLASctl_0.23-42           htmltools_0.5.6.1            
[109] pkgconfig_2.0.3               sparseMatrixStats_1.12.2     
[111] ensembldb_2.24.1              dbplyr_2.4.0                 
[113] fastmap_1.1.1                 rlang_1.1.1                  
[115] GlobalOptions_0.1.2           htmlwidgets_1.6.2            
[117] shiny_1.7.5.1                 DelayedMatrixStats_1.22.6    
[119] farver_2.1.1                  zoo_1.8-12                   
[121] jsonlite_1.8.7                BiocParallel_1.34.2          
[123] BiocSingular_1.16.0           RCurl_1.98-1.12              
[125] GenomeInfoDbData_1.2.10       dotCall64_1.1-0              
[127] patchwork_1.1.3               Rhdf5lib_1.22.1              
[129] munsell_0.5.0                 reticulate_1.34.0            
[131] stringi_1.7.12                zlibbioc_1.46.0              
[133] MASS_7.3-60                   pkgbuild_1.4.2               
[135] AnnotationHub_3.8.0           listenv_0.9.0                
[137] deldir_1.0-9                  splines_4.3.0                
[139] tensor_1.5                    hms_1.1.3                    
[141] locfit_1.5-9.8                ps_1.7.5                     
[143] spatstat.geom_3.2-7           pkgload_1.3.3                
[145] biomaRt_2.56.1                reshape2_1.4.4               
[147] ScaledMatrix_1.8.1            BiocVersion_3.17.1           
[149] XML_3.99-0.14                 BiocManager_1.30.22          
[151] foreach_1.5.2                 httpuv_1.6.12                
[153] RANN_2.6.1                    tidyr_1.3.0                  
[155] purrr_1.0.2                   polyclip_1.10-6              
[157] future_1.33.0                 clue_0.3-65                  
[159] scattermore_1.2               rsvd_1.0.5                   
[161] xtable_1.8-4                  AnnotationFilter_1.24.0      
[163] restfulr_0.0.15               later_1.3.1                  
[165] ragg_1.2.6                    viridisLite_0.4.2            
[167] tibble_3.2.1                  memoise_2.0.1                
[169] AnnotationDbi_1.62.2          GenomicAlignments_1.36.0     
[171] cluster_2.1.4                 globals_0.16.2               

Thanks in advance.

[jiangpuxuan]

I had the same problem
(addGeneIntegrationMatrix() worked in 2023 October , BUT failed now with my same Arch proj and seuratobject)