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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Error in fixupDN.if.valid(value, x@Dim) when using ReadMGATK #1749

Closed dstyaaaaaa closed 4 months ago

dstyaaaaaa commented 4 months ago

I ran mgatk tenx on my ATAC dataset and get the output like this: image And I use these outputs to run Signac. But when I ran ReadMGATK, it threw a error like this:

hemato.data <- ReadMGATK(dir = "~/atac_hemato/mgatk_sm/final/")
Reading allele counts
Reading metadata
Building matrices
Error in fixupDN.if.valid(value, x@Dim) : 
  length of Dimnames[[2]] (234676) is not equal to Dim[2] (234672)

I tried to upgrade the package like other issue mentioned, but still have the error. And compared to this, I use another data of RNA-seq but not have the error.

hemato.data <- ReadMGATK(dir = "~/pbmc_hashing/mgatk_rna/final/")
Reading allele counts
Reading metadata
Building matrices

There is session info below:

 sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

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: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] patchwork_1.2.0    Seurat_5.1.0       SeuratObject_5.0.2 sp_2.1-4          
[5] Signac_1.13.9003   ggplot2_3.5.1     

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3      rstudioapi_0.16.0       jsonlite_1.8.8         
  [4] magrittr_2.0.3          spatstat.utils_3.0-5    zlibbioc_1.48.2        
  [7] vctrs_0.6.5             ROCR_1.0-11             spatstat.explore_3.2-7 
 [10] Rsamtools_2.18.0        RCurl_1.98-1.14         RcppRoll_0.3.1         
 [13] htmltools_0.5.8.1       curl_5.2.1              sctransform_0.4.1      
 [16] parallelly_1.37.1       KernSmooth_2.23-22      desc_1.4.3             
 [19] htmlwidgets_1.6.4       ica_1.0-3               plyr_1.8.9             
 [22] plotly_4.10.4           zoo_1.8-12              igraph_2.0.3           
 [25] mime_0.12               lifecycle_1.0.4         pkgconfig_2.0.3        
 [28] Matrix_1.6-5            R6_2.5.1                fastmap_1.2.0          
 [31] GenomeInfoDbData_1.2.11 fitdistrplus_1.2-1      future_1.33.2          
 [34] shiny_1.8.1.1           digest_0.6.36           colorspace_2.1-0       
 [37] ps_1.7.6                S4Vectors_0.40.2        tensor_1.5             
 [40] RSpectra_0.16-1         irlba_2.3.5.1           GenomicRanges_1.54.1   
 [43] progressr_0.14.0        fansi_1.0.6             spatstat.sparse_3.1-0  
 [46] httr_1.4.7              polyclip_1.10-6         abind_1.4-5            
 [49] compiler_4.3.3          remotes_2.5.0           withr_3.0.0            
 [52] BiocParallel_1.36.0     fastDummies_1.7.3       pkgbuild_1.4.4         
 [55] MASS_7.3-60.0.1         tools_4.3.3             lmtest_0.9-40          
 [58] httpuv_1.6.15           future.apply_1.11.2     goftest_1.2-3          
 [61] glue_1.7.0              callr_3.7.6             nlme_3.1-164           
 [64] promises_1.3.0          grid_4.3.3              Rtsne_0.17             
 [67] cluster_2.1.6           reshape2_1.4.4          generics_0.1.3         
 [70] gtable_0.3.5            spatstat.data_3.1-2     tidyr_1.3.1            
 [73] data.table_1.15.4       utf8_1.2.4              XVector_0.42.0         
 [76] BiocGenerics_0.48.1     spatstat.geom_3.2-9     RcppAnnoy_0.0.22       
 [79] ggrepel_0.9.5           RANN_2.6.1              pillar_1.9.0           
 [82] stringr_1.5.1           spam_2.10-0             RcppHNSW_0.6.0         
 [85] later_1.3.2             splines_4.3.3           dplyr_1.1.4            
 [88] lattice_0.22-6          survival_3.5-8          deldir_2.0-4           
 [91] tidyselect_1.2.1        Biostrings_2.70.3       miniUI_0.1.1.1         
 [94] pbapply_1.7-2           gridExtra_2.3           IRanges_2.36.0         
 [97] scattermore_1.2         stats4_4.3.3            matrixStats_1.3.0      
[100] stringi_1.8.4           lazyeval_0.2.2          codetools_0.2-20       
[103] tibble_3.2.1            cli_3.6.2               uwot_0.2.2             
[106] xtable_1.8-4            reticulate_1.38.0       processx_3.8.4         
[109] munsell_0.5.1           Rcpp_1.0.12             GenomeInfoDb_1.38.8    
[112] globals_0.16.3          spatstat.random_3.2-3   png_0.1-8              
[115] parallel_4.3.3          dotCall64_1.1-1         bitops_1.0-7           
[118] listenv_0.9.1           viridisLite_0.4.2       scales_1.3.0           
[121] ggridges_0.5.6          leiden_0.4.3.1          purrr_1.0.2            
[124] crayon_1.5.3            rlang_1.1.4             cowplot_1.1.3          
[127] fastmatch_1.1-4

I wonder why and what can I do.

dstyaaaaaa commented 4 months ago

I checked the data and found I used the false reference. So sorry to disturb you!