Question

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

2

Entering edit mode

sarah.howles ▴ 20

@23328a8d

Last seen 3.0 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 • 7.2k views

ADD COMMENT • link updated 21 months ago by Hervé Pagès 16k • written 3.0 years ago by sarah.howles ▴ 20

score 2 · Answer 1 · 2021-10-19

2

Entering edit mode

Hervé Pagès 16k

@herve-pages-1542

Last seen 7 hours 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 • link 3.0 years ago Hervé Pagès 16k

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 • link 21 months ago Jack S. ▴ 50

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 • link 21 months ago Lucia ▴ 40

1

Entering edit mode

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

ADD REPLY • link 21 months ago drknwk ▴ 10

0

Entering edit mode

See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932

ADD REPLY • link 21 months ago Hervé Pagès 16k

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 • link 3.0 years ago Hervé Pagès 16k

0

Entering edit mode

Finally: https://bioconductor.org/checkResults/3.14/bioc-LATEST/GenomeInfoDb/ and https://bioconductor.org/packages/3.14/GenomeInfoDb

ADD REPLY • link 3.0 years ago Hervé Pagès 16k

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 • link 21 months ago lsoriaga2 ▴ 10

1

Entering edit mode

See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932

ADD REPLY • link 21 months ago Hervé Pagès 16k

score 0 · Answer 2 · 2023-01-31

0

Entering edit mode

Jack S. ▴ 50

@9aa6de71

Last seen 7 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 • link 21 months ago Jack S. ▴ 50