Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
2
2
Entering edit mode
sarah.howles ▴ 20
@23328a8d
Last seen 2.7 years ago
United Kingdom

Hi,

I am trying to re-run an analysis that I've used before using Seurat V4.0.4. I'm now getting this error message, I see there's previously been similar problems for mm10 due to GenomeInfoDb. Is this a new problem with hg38? I believe I'm using the most uptodate GenomeInfoDb package (1.29.8).

With thanks

counts <- Read10X_h5(filename = "..../filtered_peak_bc_matrix.h5")
metadata_atac <- read.csv(
  file = "...../singlecell.csv",
  header = TRUE,
  row.names = 1)

# the problem is here
#chrom_assay <- CreateChromatinAssay(
  counts = counts,
  sep = c(":", "-"),
  genome = 'hg38',
  fragments = '..../fragments.tsv.gz',
  min.cells = 10,
  min.features = 200
)

#Error in .order_seqlevels(chrom_sizes[, "chrom"]) : 
  !anyNA(m32) is not TRUE
Called from: .order_seqlevels(chrom_sizes[, "chrom"])

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] umap_0.2.7.0              dplyr_1.0.7               patchwork_1.1.1           ggplot2_3.3.5             Signac_1.4.0              SeuratObject_4.0.2       
 [7] Seurat_4.0.4              rlang_0.4.11              Rsamtools_2.9.1           Biostrings_2.61.2         XVector_0.33.0            hdf5r_1.3.4              
[13] limma_3.49.4              EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.17.4          AnnotationFilter_1.17.1   GenomicFeatures_1.45.2    AnnotationDbi_1.55.1     
[19] Biobase_2.53.0            GenomicRanges_1.45.0      GenomeInfoDb_1.29.8       IRanges_2.27.2            S4Vectors_0.31.5          BiocGenerics_0.39.2      

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  reticulate_1.22             tidyselect_1.1.1            RSQLite_2.2.8               htmlwidgets_1.5.4          
  [6] grid_4.1.1                  docopt_0.7.1                BiocParallel_1.27.17        Rtsne_0.15                  munsell_0.5.0              
 [11] codetools_0.2-18            ica_1.0-2                   future_1.22.1               miniUI_0.1.1.1              withr_2.4.2                
 [16] colorspace_2.0-2            filelock_1.0.2              rstudioapi_0.13             ROCR_1.0-11                 tensor_1.5                 
 [21] listenv_0.8.0               MatrixGenerics_1.5.4        slam_0.1-48                 GenomeInfoDbData_1.2.7      polyclip_1.10-0            
 [26] bit64_4.0.5                 farver_2.1.0                parallelly_1.28.1           vctrs_0.3.8                 generics_0.1.0             
 [31] BiocFileCache_2.1.1         lsa_0.73.2                  ggseqlogo_0.1               R6_2.5.1                    bitops_1.0-7               
 [36] spatstat.utils_2.2-0        cachem_1.0.6                DelayedArray_0.19.4         assertthat_0.2.1            promises_1.2.0.1           
 [41] BiocIO_1.3.0                scales_1.1.1                gtable_0.3.0                globals_0.14.0              goftest_1.2-3              
 [46] RcppRoll_0.3.0              splines_4.1.1               rtracklayer_1.53.1          lazyeval_0.2.2              spatstat.geom_2.3-0        
 [51] BiocManager_1.30.16         yaml_2.2.1                  reshape2_1.4.4              abind_1.4-5                 httpuv_1.6.3               
 [56] tools_4.1.1                 ellipsis_0.3.2              spatstat.core_2.3-0         RColorBrewer_1.1-2          ggridges_0.5.3             
 [61] Rcpp_1.0.7                  plyr_1.8.6                  progress_1.2.2              zlibbioc_1.39.0             purrr_0.3.4                
 [66] RCurl_1.98-1.5              prettyunits_1.1.1           openssl_1.4.5               rpart_4.1-15                deldir_1.0-5               
 [71] pbapply_1.5-0               cowplot_1.1.1               zoo_1.8-9                   SummarizedExperiment_1.23.5 ggrepel_0.9.1              
 [76] cluster_2.1.2               magrittr_2.0.1              data.table_1.14.2           RSpectra_0.16-0             scattermore_0.7            
 [81] lmtest_0.9-38               RANN_2.6.1                  SnowballC_0.7.0             ProtGenerics_1.25.1         fitdistrplus_1.1-6         
 [86] matrixStats_0.61.0          hms_1.1.1                   mime_0.12                   xtable_1.8-4                XML_3.99-0.8               
 [91] sparsesvd_0.2               gridExtra_2.3               compiler_4.1.1              biomaRt_2.49.6              tibble_3.1.5               
 [96] KernSmooth_2.23-20          crayon_1.4.1                htmltools_0.5.2             mgcv_1.8-38                 later_1.3.0                
[101] tidyr_1.1.4                 DBI_1.1.1                   tweenr_1.0.2                dbplyr_2.1.1                MASS_7.3-54                
[106] rappdirs_0.3.3              Matrix_1.3-4                parallel_4.1.1              igraph_1.2.7                pkgconfig_2.0.3            
[111] GenomicAlignments_1.29.0    plotly_4.10.0               spatstat.sparse_2.0-0       xml2_1.3.2                  stringr_1.4.0              
[116] digest_0.6.28               sctransform_0.3.2           RcppAnnoy_0.0.19            spatstat.data_2.1-0         leiden_0.3.9               
[121] fastmatch_1.1-3             uwot_0.1.10                 restfulr_0.0.13             curl_4.3.2                  shiny_1.7.1                
[126] rjson_0.2.20                lifecycle_1.0.1             nlme_3.1-153                jsonlite_1.7.2              askpass_1.1                
[131] viridisLite_0.4.0           fansi_0.5.0                 pillar_1.6.4                lattice_0.20-45             KEGGREST_1.33.0            
[136] fastmap_1.1.0               httr_1.4.2                  survival_3.2-13             glue_1.4.2                  qlcMatrix_0.9.7            
[141] png_0.1-7                   bit_4.0.4                   ggforce_0.3.3               stringi_1.7.5               blob_1.2.2                 
[146] memoise_2.0.0               irlba_2.3.3                 future.apply_1.8.1
GenomeInfoDb • 6.9k views
ADD COMMENT
2
Entering edit mode
@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

Hi,

See this issue on GitHub. It's now fixed in GenomeInfoDb 1.29.10 (see this commit). GenomeInfoDb 1.29.10 should become available in a couple of hours to BioC 3.14 users via BiocManager::install().

Unfortunately the fix cannot be backported to BioC 3.13 because we froze it last week so we can no longer touch it.

The good news is that BioC 3.14 will be released next week.

Cheers,

H.

ADD COMMENT
5
Entering edit mode

Getting the same error again. My code worked fine last night but it fails at this line today:

seqlevelsStyle(annotations) <- 'UCSC'

Error in .order_seqlevels(chrom_sizes[, "chrom"]): !anyNA(m32) is not TRUE

ADD REPLY
4
Entering edit mode

I am getting the same error from yesterday. Does somebody know what it is going on? or How can we fix it? Or is it a matter of time to get fixed?

annotation <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)

|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=23s
Warning: The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress this warning.)Warning: The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress this warning.)Warning: The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress this warning.)Warning: The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress this warning.)Warning: The 2 combined objects have no sequence levels in common. (Use

seqlevelsStyle(annotation) <- "UCSC"
    Error in .order_seqlevels(chrom_sizes[, "chrom"]) : 
      !anyNA(m32) is not TRUE
ADD REPLY
1
Entering edit mode

Exact same problem here suddenly. Hope someone will have a fix soon!

ADD REPLY
0
Entering edit mode

I spoke too soon, sorry: https://bioconductor.org/checkResults/3.14/bioc-LATEST/GenomeInfoDb/

I committed another fix that _should_ address this but that means we're going to have to wait another 24 hours before we can install it with BiocManager::install().

Sorry for the inconvenience,

H.

ADD REPLY
1
Entering edit mode

Hello, This error seems to have returned (R 4.2.2 BioC 3.16.0)?
The same code block worked without error until today.

> library(Signac)
> library(EnsDb.Hsapiens.v86)
> library(BSgenome.Hsapiens.UCSC.hg38)
> annotation <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=32s  
There were 24 warnings (use warnings() to see them)
> seqlevelsStyle(annotation) <- "UCSC"
Error in .order_seqlevels(chrom_sizes[, "chrom"]) :
!anyNA(m32) is not TRUE
19.
stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
18.
stopifnot(!anyNA(m32)) at hg38.R#37
17.
.order_seqlevels(chrom_sizes[, "chrom"]) at hg38.R#69
16.
FETCH_ORDERED_CHROM_SIZES(goldenPath.url = goldenPath.url)
15.
.fetch_raw_chrom_info_from_UCSC(GENOME, ASSEMBLED_MOLECULES,
CIRC_SEQS, FETCH_ORDERED_CHROM_SIZES, goldenPath.url = goldenPath.url)
14.
.get_raw_chrom_info_for_registered_UCSC_genome(GENOME, ASSEMBLED_MOLECULES,
vars$CIRC_SEQS, FETCH_ORDERED_CHROM_SIZES = vars$FETCH_ORDERED_CHROM_SIZES,
assembled.molecules.only = assembled.molecules.only, goldenPath.url = goldenPath.url,
recache = recache)
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")

> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-openmp/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-openmp/liblapack.so.3

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8    
 [5] LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C             
 [9] LC_ADDRESS=C           LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.4 BSgenome_1.66.2                   rtracklayer_1.58.0               
 [4] Biostrings_2.66.0                 XVector_0.38.0                    EnsDb.Hsapiens.v86_2.99.0        
 [7] ensembldb_2.22.0                  AnnotationFilter_1.22.0           GenomicFeatures_1.50.4           
[10] AnnotationDbi_1.60.0              Biobase_2.58.0                    GenomicRanges_1.50.2             
[13] GenomeInfoDb_1.34.7               IRanges_2.32.0                    S4Vectors_0.36.1                 
[16] BiocGenerics_0.44.0               Signac_1.9.0                     

loaded via a namespace (and not attached):
  [1] colorspace_2.1-0            deldir_1.0-6                rjson_0.2.21               
  [4] ellipsis_0.3.2              htmlTable_2.4.1             biovizBase_1.46.0          
  [7] base64enc_0.1-3             dichromat_2.0-0.1           rstudioapi_0.14            
 [10] listenv_0.9.0               bit64_4.0.5                 fansi_1.0.4                
 [13] xml2_1.3.3                  codetools_0.2-18            splines_4.2.2              
 [16] cachem_1.0.6                knitr_1.42                  RcppRoll_0.3.0             
 [19] Formula_1.2-4               Rsamtools_2.14.0            cluster_2.1.4              
 [22] dbplyr_2.3.0                png_0.1-8                   compiler_4.2.2             
 [25] httr_1.4.4                  backports_1.4.1             assertthat_0.2.1           
 [28] SeuratObject_4.1.3          Matrix_1.5-3                fastmap_1.1.0              
 [31] lazyeval_0.2.2              cli_3.6.0                   htmltools_0.5.4            
 [34] prettyunits_1.1.1           tools_4.2.2                 gtable_0.3.1               
 [37] glue_1.6.2                  GenomeInfoDbData_1.2.9      dplyr_1.0.10               
 [40] rappdirs_0.3.3              fastmatch_1.1-3             Rcpp_1.0.10                
 [43] vctrs_0.5.2                 progressr_0.13.0            xfun_0.36                  
 [46] stringr_1.5.0               globals_0.16.2              lifecycle_1.0.3            
 [49] irlba_2.3.5.1               restfulr_0.0.15             renv_0.16.0                
 [52] XML_3.99-0.13               future_1.30.0               zlibbioc_1.44.0            
 [55] scales_1.2.1                VariantAnnotation_1.44.0    hms_1.1.2                  
 [58] MatrixGenerics_1.10.0       ProtGenerics_1.30.0         parallel_4.2.2             
 [61] SummarizedExperiment_1.28.0 RColorBrewer_1.1-3          yaml_2.3.7                 
 [64] curl_5.0.0                  gridExtra_2.3               memoise_2.0.1              
 [67] pbapply_1.7-0               ggplot2_3.4.0               rpart_4.1.19               
 [70] biomaRt_2.54.0              latticeExtra_0.6-30         stringi_1.7.12             
 [73] RSQLite_2.2.20              BiocIO_1.8.0                checkmate_2.1.0            
 [76] filelock_1.0.2              BiocParallel_1.32.5         rlang_1.0.6                
 [79] pkgconfig_2.0.3             bitops_1.0-7                matrixStats_0.63.0         
 [82] lattice_0.20-45             purrr_1.0.1                 htmlwidgets_1.6.1          
 [85] GenomicAlignments_1.34.0    patchwork_1.1.2             bit_4.0.5                  
 [88] tidyselect_1.2.0            parallelly_1.34.0           magrittr_2.0.3             
 [91] R6_2.5.1                    generics_0.1.3              Hmisc_4.7-2                
 [94] DelayedArray_0.24.0         DBI_1.1.3                   foreign_0.8-82             
 [97] pillar_1.8.1                nnet_7.3-18                 survival_3.4-0             
[100] KEGGREST_1.38.0             RCurl_1.98-1.9              sp_1.6-0                   
[103] tibble_3.1.8                future.apply_1.10.0         crayon_1.5.2               
[106] interp_1.1-3                utf8_1.2.2                  BiocFileCache_2.6.0        
[109] jpeg_0.1-10                 progress_1.2.2              grid_4.2.2                 
[112] data.table_1.14.6           blob_1.2.3                  digest_0.6.31              
[115] tidyr_1.3.0                 munsell_0.5.
ADD REPLY
0
Entering edit mode
Jack S. ▴ 50
@9aa6de71
Last seen 3 months ago
United States

Apparently, UCSC changed their assembly again. See the discussion on the Bioconductor/GenomeInfoDB Github page. The solution is explained in this comment.

ADD COMMENT

Login before adding your answer.

Traffic: 770 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6