Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
1
2
Entering edit mode
sarah.howles ▴ 20
@23328a8d
Last seen 5 weeks 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 • 762 views
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2
Entering edit mode
@herve-pages-1542
Last seen 3 days 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.

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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.

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