Problem with loading a h5seurat file with LoadH5Seurat

[ghost]

Hi!

I am trying to convert a h5ad file (AnnData v0.8) that I obtained from here:

https://datasets.cellxgene.cziscience.com/3ab47484-a3eb-4f6a-beea-670e1a8fc1e8.h5ad

into a Seurat object using a method that had been suggested previously. When trying to load the resulting h5seurat object I am stuck with a warning message and no Seurat object is created. Anybody an idea how to solve this? Thank you!

My code:

library(SeuratDisk)
Convert("Full_lung_cell_atlas_with_disease.h5ad", "h5seurat")
seuratObj <- LoadH5Seurat("Full_lung_cell_atlas_with_disease.h5seurat")

My console output so far including the (error) messages:

library(SeuratDisk)
Registered S3 method overwritten by 'SeuratDisk':
method from
as.sparse.H5Group Seurat
Convert("Full_lung_cell_atlas_with_disease.h5ad", "h5seurat")
Warning: Unknown file type: h5adWarning: 'assay' not set, setting to 'RNA'Creating h5Seurat file for version 3.1.5.9900
Adding X as data
Adding raw/X as counts
Adding meta.features from raw/var
Adding X_scanvi_emb as cell embeddings for scanvi_emb
Adding X_umap as cell embeddings for umap
Adding batch_condition to miscellaneous data
Adding citation to miscellaneous data
Adding default_embedding to miscellaneous data
Adding schema_reference to miscellaneous data
Adding schema_version to miscellaneous data
Adding title to miscellaneous data
Adding layer soupX as data in assay soupX
Adding layer soupX as counts in assay soupX
seuratObj <- LoadH5Seurat("Full_lung_cell_atlas_with_disease.h5seurat")
Validating h5Seurat file
Initializing RNA with data
Warning: NAs introduced by coercion to integer rangeError in sparseMatrix(i = x[["indices"]][] + 1, p = x[["indptr"]][], x = x[["data"]][], :
'p' must be a nondecreasing vector c(0, ...)

Session info:

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] SeuratDisk_0.0.0.9021 sceasy_0.0.7 reticulate_1.34.0
[4] SeuratObject_5.0.1 sp_2.1-2

loaded via a namespace (and not attached):
[1] deldir_2.0-2 pbapply_1.7-2 gridExtra_2.3
[4] rlang_1.1.3 magrittr_2.0.3 RcppAnnoy_0.0.21
[7] spatstat.geom_3.2-7 matrixStats_1.2.0 ggridges_0.5.5
[10] compiler_4.3.2 png_0.1-8 vctrs_0.6.5
[13] reshape2_1.4.4 hdf5r_1.3.9 stringr_1.5.1
[16] crayon_1.5.2 pkgconfig_2.0.3 fastmap_1.1.1
[19] ellipsis_0.3.2 utf8_1.2.4 promises_1.2.1
[22] bit_4.0.5 purrr_1.0.2 xfun_0.41
[25] jsonlite_1.8.8 goftest_1.2-3 later_1.3.2
[28] spatstat.utils_3.0-4 irlba_2.3.5.1 parallel_4.3.2
[31] cluster_2.1.6 R6_2.5.1 ica_1.0-3
[34] stringi_1.8.3 RColorBrewer_1.1-3 spatstat.data_3.0-4
[37] parallelly_1.36.0 lmtest_0.9-40 scattermore_1.2
[40] Rcpp_1.0.12 knitr_1.45 tensor_1.5
[43] future.apply_1.11.1 zoo_1.8-12 sctransform_0.4.1
[46] httpuv_1.6.13 Matrix_1.6-5 splines_4.3.2
[49] igraph_1.6.0 tidyselect_1.2.0 abind_1.4-5
[52] rstudioapi_0.15.0 spatstat.random_3.2-2 codetools_0.2-19
[55] miniUI_0.1.1.1 spatstat.explore_3.2-5 listenv_0.9.0
[58] lattice_0.22-5 tibble_3.2.1 plyr_1.8.9
[61] shiny_1.8.0 withr_3.0.0 ROCR_1.0-11
[64] Rtsne_0.17 future_1.33.1 fastDummies_1.7.3
[67] survival_3.5-7 polyclip_1.10-6 fitdistrplus_1.1-11
[70] pillar_1.9.0 Seurat_5.0.1 KernSmooth_2.23-22
[73] plotly_4.10.4 generics_0.1.3 RcppHNSW_0.5.0
[76] ggplot2_3.4.4 munsell_0.5.0 scales_1.3.0
[79] globals_0.16.2 xtable_1.8-4 glue_1.7.0
[82] lazyeval_0.2.2 tools_4.3.2 data.table_1.14.10
[85] RSpectra_0.16-1 RANN_2.6.1 leiden_0.4.3.1
[88] dotCall64_1.1-1 cowplot_1.1.2 grid_4.3.2
[91] tidyr_1.3.0 colorspace_2.1-0 nlme_3.1-164
[94] patchwork_1.2.0 cli_3.6.2 spatstat.sparse_3.0-3
[97] spam_2.10-0 fansi_1.0.6 viridisLite_0.4.2
[100] dplyr_1.1.4 uwot_0.1.16 gtable_0.3.4
[103] digest_0.6.34 progressr_0.14.0 ggrepel_0.9.5
[106] htmlwidgets_1.6.4 htmltools_0.5.7 lifecycle_1.0.4
[109] httr_1.4.7 mime_0.12 bit64_4.0.5
[112] MASS_7.3-60