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qlan20 opened this issue Jun 28, 2021 · 7 comments
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Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE #687

qlan20 opened this issue Jun 28, 2021 · 7 comments
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@qlan20
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qlan20 commented Jun 28, 2021 •
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Dear Tim,
An error occured with CreateChromatinAssay and seqlevels when I was trying out the vignette on SNARE-seq. I was wondering whether there's any setting issues? (good with vignette on 10x Multiomics) Thanks!

snare[['ATAC']] <- CreateChromatinAssay(
+   counts = atac,
+   sep = c(":", "-"),
+   genome = "mm10",
+   fragments = fragments
+ )

or

seqlevelsStyle(annotations) <- 'UCSC'

The error:

 Error in .order_seqlevels(chrom_sizes[, "chrom"]) : 
  !anyNA(m31) is not TRUE 
17.
stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p))) 
16.
stopifnot(!anyNA(m31)) at mm10.R#24
15.
.order_seqlevels(chrom_sizes[, "chrom"]) at mm10.R#42
14.
GET_CHROM_SIZES(goldenPath.url = goldenPath.url) 
13.
.get_chrom_info_for_registered_UCSC_genome(script_path, assembled.molecules.only = assembled.molecules.only, 
    map.NCBI = map.NCBI, add.ensembl.col = add.ensembl.col, goldenPath.url = goldenPath.url, 
    recache = recache) 
12.
getChromInfoFromUCSC(new_genome, map.NCBI = TRUE) 
11.
(function (seqlevels, genome, new_style) 
{
    ans <- DataFrame(seqlevels = seqlevels, genome = genome)
    if (is.na(genome) || !(new_style %in% c("NCBI", "RefSeq",  ... 
10.
mapply(FUN = FUN, ..., MoreArgs = MoreArgs, SIMPLIFY = SIMPLIFY, 
    USE.NAMES = USE.NAMES) 
9.
eval(mc, env) 
8.
eval(mc, env) 
7.
eval(mc, env) 
6.
standardGeneric("mapply") 
5.
mapply(.set_seqlevelsStyle_from_seqlevels_and_genome, genome2seqlevels, 
    names(genome2seqlevels), MoreArgs = list(value), SIMPLIFY = FALSE, 
    USE.NAMES = FALSE) 
4.
`seqlevelsStyle<-`(`*tmp*`, value = value) 
3.
`seqlevelsStyle<-`(`*tmp*`, value = value) 
2.
`seqlevelsStyle<-`(`*tmp*`, value = "UCSC") 
1.
`seqlevelsStyle<-`(`*tmp*`, value = "UCSC")

The sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    
system code page: 65001

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

other attached packages:
 [1] EnsDb.Mmusculus.v79_2.99.0       
 [2] ggplot2_3.3.5                    
 [3] BSgenome.Hsapiens.UCSC.hg38_1.4.3
 [4] BSgenome_1.58.0                  
 [5] rtracklayer_1.49.5               
 [6] Biostrings_2.58.0                
 [7] XVector_0.30.0                   
 [8] EnsDb.Hsapiens.v86_2.99.0        
 [9] ensembldb_2.14.1                 
[10] AnnotationFilter_1.14.0          
[11] GenomicFeatures_1.42.3           
[12] AnnotationDbi_1.52.0             
[13] Biobase_2.50.0                   
[14] Seurat_4.0.2                     
[15] Signac_1.2.1                     
[16] SeuratObject_4.0.1               
[17] Matrix_1.3-4                     
[18] GenomicRanges_1.42.0             
[19] GenomeInfoDb_1.26.7              
[20] IRanges_2.24.1                   
[21] S4Vectors_0.28.1                 
[22] BiocGenerics_0.36.1              

loaded via a namespace (and not attached):
  [1] utf8_1.2.1                 
  [2] reticulate_1.20            
  [3] tidyselect_1.1.1           
  [4] RSQLite_2.2.7              
  [5] htmlwidgets_1.5.3          
  [6] grid_4.0.3                 
  [7] docopt_0.7.1               
  [8] BiocParallel_1.24.1        
  [9] Rtsne_0.15                 
 [10] devtools_2.4.2             
 [11] munsell_0.5.0              
 [12] codetools_0.2-16           
 [13] ica_1.0-2                  
 [14] future_1.21.0              
 [15] miniUI_0.1.1.1             
 [16] withr_2.4.2                
 [17] colorspace_2.0-1           
 [18] knitr_1.33                 
 [19] rstudioapi_0.13            
 [20] ROCR_1.0-11                
 [21] tensor_1.5                 
 [22] listenv_0.8.0              
 [23] MatrixGenerics_1.2.1       
 [24] slam_0.1-48                
 [25] GenomeInfoDbData_1.2.4     
 [26] polyclip_1.10-0            
 [27] bit64_4.0.5                
 [28] farver_2.1.0               
 [29] rprojroot_2.0.2            
 [30] parallelly_1.26.0          
 [31] vctrs_0.3.8                
 [32] generics_0.1.0             
 [33] xfun_0.24                  
 [34] biovizBase_1.38.0          
 [35] BiocFileCache_1.14.0       
 [36] lsa_0.73.2                 
 [37] ggseqlogo_0.1              
 [38] R6_2.5.0                   
 [39] DelayedArray_0.16.3        
 [40] bitops_1.0-7               
 [41] spatstat.utils_2.1-0       
 [42] cachem_1.0.5               
 [43] assertthat_0.2.1           
 [44] promises_1.2.0.1           
 [45] scales_1.1.1               
 [46] nnet_7.3-14                
 [47] gtable_0.3.0               
 [48] globals_0.14.0             
 [49] processx_3.5.2             
 [50] goftest_1.2-2              
 [51] rlang_0.4.11               
 [52] RcppRoll_0.3.0             
 [53] splines_4.0.3              
 [54] lazyeval_0.2.2             
 [55] dichromat_2.0-0            
 [56] checkmate_2.0.0            
 [57] spatstat.geom_2.1-0        
 [58] reshape2_1.4.4             
 [59] abind_1.4-5                
 [60] backports_1.2.1            
 [61] httpuv_1.6.1               
 [62] Hmisc_4.5-0                
 [63] tools_4.0.3                
 [64] usethis_2.0.1              
 [65] ellipsis_0.3.2             
 [66] spatstat.core_2.1-2        
 [67] RColorBrewer_1.1-2         
 [68] sessioninfo_1.1.1          
 [69] ggridges_0.5.3             
 [70] Rcpp_1.0.6                 
 [71] plyr_1.8.6                 
 [72] base64enc_0.1-3            
 [73] progress_1.2.2             
 [74] zlibbioc_1.36.0            
 [75] purrr_0.3.4                
 [76] RCurl_1.98-1.3             
 [77] ps_1.6.0                   
 [78] prettyunits_1.1.1          
 [79] rpart_4.1-15               
 [80] openssl_1.4.4              
 [81] deldir_0.2-10              
 [82] pbapply_1.4-3              
 [83] cowplot_1.1.1              
 [84] zoo_1.8-9                  
 [85] SummarizedExperiment_1.20.0
 [86] ggrepel_0.9.1              
 [87] cluster_2.1.0              
 [88] fs_1.5.0                   
 [89] magrittr_2.0.1             
 [90] data.table_1.14.0          
 [91] scattermore_0.7            
 [92] lmtest_0.9-38              
 [93] RANN_2.6.1                 
 [94] SnowballC_0.7.0            
 [95] ProtGenerics_1.22.0        
 [96] fitdistrplus_1.1-5         
 [97] matrixStats_0.59.0         
 [98] pkgload_1.2.1              
 [99] hms_1.1.0                  
[100] patchwork_1.1.1            
[101] mime_0.10                  
[102] xtable_1.8-4               
[103] XML_3.99-0.6               
[104] jpeg_0.1-8.1               
[105] sparsesvd_0.2              
[106] gridExtra_2.3              
[107] testthat_3.0.3             
[108] compiler_4.0.3             
[109] biomaRt_2.46.3             
[110] tibble_3.1.2               
[111] KernSmooth_2.23-17         
[112] crayon_1.4.1               
[113] htmltools_0.5.1.1          
[114] mgcv_1.8-33                
[115] later_1.2.0                
[116] Formula_1.2-4              
[117] tidyr_1.1.3                
[118] DBI_1.1.1                  
[119] tweenr_1.0.2               
[120] dbplyr_2.1.1               
[121] rappdirs_0.3.3             
[122] MASS_7.3-53                
[123] cli_2.5.0                  
[124] igraph_1.2.6               
[125] pkgconfig_2.0.3            
[126] GenomicAlignments_1.26.0   
[127] foreign_0.8-80             
[128] plotly_4.9.4.1             
[129] spatstat.sparse_2.0-0      
[130] xml2_1.3.2                 
[131] VariantAnnotation_1.36.0   
[132] stringr_1.4.0              
[133] callr_3.7.0                
[134] digest_0.6.27              
[135] sctransform_0.3.2          
[136] RcppAnnoy_0.0.18           
[137] spatstat.data_2.1-0        
[138] leiden_0.3.8               
[139] fastmatch_1.1-0            
[140] htmlTable_2.2.1            
[141] uwot_0.1.10                
[142] curl_4.3.1                 
[143] shiny_1.6.0                
[144] Rsamtools_2.6.0            
[145] lifecycle_1.0.0            
[146] nlme_3.1-149               
[147] jsonlite_1.7.2             
[148] desc_1.3.0                 
[149] viridisLite_0.4.0          
[150] askpass_1.1                
[151] fansi_0.5.0                
[152] pillar_1.6.1               
[153] lattice_0.20-41            
[154] fastmap_1.1.0              
[155] httr_1.4.2                 
[156] pkgbuild_1.2.0             
[157] survival_3.2-7             
[158] glue_1.4.2                 
[159] remotes_2.4.0              
[160] qlcMatrix_0.9.7            
[161] png_0.1-7                  
[162] bit_4.0.4                  
[163] ggforce_0.3.3              
[164] stringi_1.5.3              
[165] blob_1.2.1                 
[166] latticeExtra_0.6-29        
[167] memoise_2.0.0              
[168] dplyr_1.0.6                
[169] irlba_2.3.3                
[170] future.apply_1.7.0
@qlan20 qlan20 added the bug Something isn't working label Jun 28, 2021
@timoast
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timoast commented Jun 28, 2021

This appears to be an issue with GenomeInfoDb rather than Signac, the following also fails:

library(EnsDb.Mmusculus.v79)
library(GenomeInfoDb)
annotations <- genes(EnsDb.Mmusculus.v79)
seqlevelsStyle(annotations) <- 'UCSC'

Please raise an issue on the bioconductor support forum instead

@timoast timoast closed this as completed Jun 28, 2021
This was referenced Jun 28, 2021
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@timoast
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timoast commented Jun 30, 2021

Linking to the GenomeInfoDb issue: Bioconductor/GenomeInfoDb#27

This was referenced Jun 30, 2021
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@timoast timoast mentioned this issue Jul 22, 2021
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@timoast timoast mentioned this issue Aug 25, 2021
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@yuhsinhsieh-josch yuhsinhsieh-josch mentioned this issue Oct 18, 2021
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@timoast timoast mentioned this issue Feb 8, 2023
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@Dragonmasterx87
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Dragonmasterx87 commented Feb 8, 2023 •
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Just an update, I ran into this issue as well. The solution was updating GenomeInfoDb using remotes. Somehow the version on CRAN still has issues.

# First remove old version
remove.packages("BiocManager", lib=.libPaths("PATH_to_your_library_containing_GenomeInfoDb"))
BiocManager::valid("GenomeInfoDb") # This should throw an error if not repeat the remove.packages step

# Install the version that works as of 2/8/2023
remotes::install_github("Bioconductor/GenomeInfoDb")
BiocManager::valid("GenomeInfoDb") 
packageVersion("genomeInfoDb") # as of 02/08/2022 should show v1.35.15

Doing BiocManager::install("GenomeInfoDb") doesn't work.

Note to my future self:
I told you to annotate solutions in your script, now look at you looking for solutions to problems you already resolved. Fool.

@cmiciano
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thank you @Dragonmasterx87 for the helpful solution, i was able to get seqlevelsStyle(annotations) <- 'UCSC'
working again after updating GenomeInfoDb with the remotes version you provided.

@JohnWang1997
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thank you, @Dragonmasterx87 , the solution solved the issue that GenomeInfoDb (>=1.34.8) cannot be installed through BiocManager (3.14) in R (4.1.2).

@Dragonmasterx87
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Cheers guys glad it worked.

@linkous123
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Cheers guys glad it worked.

Just an update, I ran into this issue as well. The solution was updating GenomeInfoDb using remotes. Somehow the version on CRAN still has issues.

# First remove old version
remove.packages("BiocManager", lib=.libPaths("PATH_to_your_library_containing_GenomeInfoDb"))
BiocManager::valid("GenomeInfoDb") # This should throw an error if not repeat the remove.packages step

# Install the version that works as of 2/8/2023
remotes::install_github("Bioconductor/GenomeInfoDb")
BiocManager::valid("GenomeInfoDb") 
packageVersion("genomeInfoDb") # as of 02/08/2022 should show v1.35.15

Doing BiocManager::install("GenomeInfoDb") doesn't work.

Note to my future self: I told you to annotate solutions in your script, now look at you looking for solutions to problems you already resolved. Fool.

hi, I follow your method to install GenomeInfoDb==1.35.15, it thorw another error, have you some ideas? thinks!

my code :
library(Seurat)
library(Signac)
library(EnsDb.Hsapiens.v86)
library(BSgenome.Hsapiens.UCSC.hg38)
library(future)
library(ggplot2)
library(patchwork)

annot <- GetGRangesFromEnsDb(EnsDb.Hsapiens.v86)
seqlevelsStyle(annot) <- "UCSC"

the return:

seqlevelsStyle(annot) <- "UCSC"
Error in stop_if(is.null(NCBI_assembly_info), ""assembly_accession" field in 'NCBI_LINKER' must ", :
Error in UCSC genome registration file 'canFam6.R':
"assembly_accession" field in 'NCBI_LINKER' must be associated with a registered NCBI assembly

@Nick-Eagles Nick-Eagles mentioned this issue Jul 5, 2023
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@timoast @JohnWang1997 @cmiciano @Dragonmasterx87 @qlan20 @linkous123