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20 hours ago •
mojaveazure
mojaveazure
HDF5-API Errors: error #000: H5Ocopy.c in H5Ocopy(): line 240: unable to copy object
Hi, I am unable to convert my h5ad object to h5seurat. I'd be grateful for any pointers about how to get this working. Here is the code I used:
library(Seurat)
library(SeuratDisk)
Convert("/Users/sargent/projects/Bioinf_CRO/ADA/data/byrd-h5ad_for_cellphonedb/38682c3f/38682c3f_healthy_normalized.h5ad", dest = "h5seurat", overwrite = FALSE)
Here is the output:
Warning: Unknown file type: h5ad
Warning: 'assay' not set, setting to 'RNA'
Creating h5Seurat file for version 3.1.5.9900
Adding X as data
Adding X as data
Adding X as counts
Adding X as counts
Adding meta.features from var
Adding meta.features from var
Error in dfile$obj_copy_from(src_loc = source, src_name = "obs", dst_name = "meta.data") :
HDF5-API Errors:
error #000: H5Ocopy.c in H5Ocopy(): line 240: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
error #001: H5VLcallback.c in H5VL_object_copy(): line 5495: object copy failed
class: HDF5
major: Virtual Object Layer
minor: Unable to copy object
error #002: H5VLcallback.c in H5VL__object_copy(): line 5456: object copy failed
class: HDF5
major: Virtual Object Layer
minor: Unable to copy object
error #003: H5VLnative_object.c in H5VL__native_object_copy(): line 125: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
error #004: H5Ocopy.c in H5O__copy(): line 301: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
error #005: H5Ocopy.c in H5O__copy_obj(): line 1196: unable to copy object
class: HDF5
maj
Error in dfile$obj_copy_from(src_loc = source, src_name = "obs", dst_name = "meta.data") :
HDF5-API Errors:
error #000: H5Ocopy.c in H5Ocopy(): line 240: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
error #001: H5VLcallback.c in H5VL_object_copy(): line 5495: object copy failed
class: HDF5
major: Virtual Object Layer
minor: Unable to copy object
error #002: H5VLcallback.c in H5VL__object_copy(): line 5456: object copy failed
class: HDF5
major: Virtual Object Layer
minor: Unable to copy object
error #003: H5VLnative_object.c in H5VL__native_object_copy(): line 125: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
error #004: H5Ocopy.c in H5O__copy(): line 301: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
error #005: H5Ocopy.c in H5O__copy_obj(): line 1196: unable to copy object
class: HDF5
maj
Error in private$closeFun(id) : HDF5-API Errors:
error #000: H5F.c in H5Fclose(): line 711: decrementing file ID failed
class: HDF5
major: File accessibility
minor: Unable to close file
error #001: H5Iint.c in H5I_dec_app_ref(): line 1018: can't decrement ID ref count
class: HDF5
major: Object atom
minor: Unable to decrement reference count
error #002: H5Fint.c in H5F__close_cb(): line 251: unable to close file
class: HDF5
major: File accessibility
minor: Unable to close file
error #003: H5VLcallback.c in H5VL_file_close(): line 3983: file close failed
class: HDF5
major: Virtual Object Layer
minor: Unable to close file
error #004: H5VLcallback.c in H5VL__file_close(): line 3952: file close failed
class: HDF5
major: Virtual Object Layer
minor: Unable to close file
error #005: H5VLnative_file.c in H5VL__native_file_close(): line 838: can't close file
clas
Error in private$closeFun(id) : HDF5-API Errors:
error #000: H5F.c in H5Fclose(): line 711: decrementing file ID failed
class: HDF5
major: File accessibility
minor: Unable to close file
error #001: H5Iint.c in H5I_dec_app_ref(): line 1018: can't decrement ID ref count
class: HDF5
major: Object atom
minor: Unable to decrement reference count
error #002: H5Fint.c in H5F__close_cb(): line 251: unable to close file
class: HDF5
major: File accessibility
minor: Unable to close file
error #003: H5VLcallback.c in H5VL_file_close(): line 3983: file close failed
class: HDF5
major: Virtual Object Layer
minor: Unable to close file
error #004: H5VLcallback.c in H5VL__file_close(): line 3952: file close failed
class: HDF5
major: Virtual Object Layer
minor: Unable to close file
error #005: H5VLnative_file.c in H5VL__native_file_close(): line 838: can't close file
clas
A h5seurat file is created but when I try to read it in using the following command:
healthy_seu <- LoadH5Seurat("/Users/sargent/projects/Bioinf_CRO/ADA/data/byrd-h5ad_for_cellphonedb/38682c3f/38682c3f_healthy_normalized.h5seurat")
I get the following error:
Validating h5Seurat file
Error: Cannot find dataset with cell names
Error: Cannot find dataset with cell names
Here is my sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Users/sargent/miniconda3/envs/seurat/lib/libopenblasp-r0.3.21.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeuratDisk_0.0.0.9019 sp_1.5-0 SeuratObject_4.1.1 Seurat_4.1.1
loaded via a namespace (and not attached):
[1] Rtsne_0.16 colorspace_2.0-3 deldir_1.0-6 ellipsis_0.3.2 ggridges_0.5.4
[6] rstudioapi_0.14 spatstat.data_2.2-0 leiden_0.4.3 listenv_0.8.0 ggrepel_0.9.1
[11] bit64_4.0.5 fansi_1.0.3 codetools_0.2-18 splines_4.0.5 polyclip_1.10-0
[16] jsonlite_1.8.0 ica_1.0-3 cluster_2.1.3 png_0.1-7 rgeos_0.5-9
[21] uwot_0.1.14 shiny_1.7.2 sctransform_0.3.4 spatstat.sparse_2.1-1 compiler_4.0.5
[26] httr_1.4.4 assertthat_0.2.1 Matrix_1.4-1 fastmap_1.1.0 lazyeval_0.2.2
[31] cli_3.4.1 later_1.2.0 htmltools_0.5.3 tools_4.0.5 igraph_1.3.4
[36] gtable_0.3.1 glue_1.6.2 RANN_2.6.1 reshape2_1.4.4 dplyr_1.0.10
[41] Rcpp_1.0.9 scattermore_0.8 vctrs_0.4.1 nlme_3.1-159 progressr_0.11.0
[46] lmtest_0.9-40 spatstat.random_2.2-0 stringr_1.4.1 globals_0.16.1 mime_0.12
[51] miniUI_0.1.1.1 lifecycle_1.0.2 irlba_2.3.5 goftest_1.2-3 future_1.28.0
[56] MASS_7.3-58.1 zoo_1.8-11 scales_1.2.1 spatstat.core_2.4-4 promises_1.2.0.1
[61] spatstat.utils_2.3-1 parallel_4.0.5 RColorBrewer_1.1-3 yaml_2.3.5 reticulate_1.28
[66] pbapply_1.5-0 gridExtra_2.3 ggplot2_3.3.6 rpart_4.1.16 stringi_1.7.8
[71] rlang_1.0.6 pkgconfig_2.0.3 matrixStats_0.62.0 lattice_0.20-45 ROCR_1.0-11
[76] purrr_0.3.4 tensor_1.5 patchwork_1.1.2 htmlwidgets_1.5.4 cowplot_1.1.1
[81] bit_4.0.4 tidyselect_1.1.2 parallelly_1.32.1 RcppAnnoy_0.0.19 plyr_1.8.7
[86] magrittr_2.0.3 R6_2.5.1 generics_0.1.3 DBI_1.1.3 pillar_1.8.1
[91] withr_2.5.0 mgcv_1.8-40 fitdistrplus_1.1-8 survival_3.4-0 abind_1.4-5
[96] tibble_3.1.8 future.apply_1.9.1 crayon_1.5.1 hdf5r_1.3.6 KernSmooth_2.23-20
[101] utf8_1.2.2 spatstat.geom_2.4-0 plotly_4.10.0 grid_4.0.5 data.table_1.14.2
[106] digest_0.6.29 xtable_1.8-4 tidyr_1.2.1 httpuv_1.6.6 munsell_0.5.0
[111] viridisLite_0.4.1
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Users/sargent/miniconda3/envs/seurat/lib/libopenblasp-r0.3.21.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeuratDisk_0.0.0.9019 sp_1.5-0 SeuratObject_4.1.1 Seurat_4.1.1
loaded via a namespace (and not attached):
[1] Rtsne_0.16 colorspace_2.0-3 deldir_1.0-6 ellipsis_0.3.2 ggridges_0.5.4
[6] rstudioapi_0.14 spatstat.data_2.2-0 leiden_0.4.3 listenv_0.8.0 ggrepel_0.9.1
[11] bit64_4.0.5 fansi_1.0.3 codetools_0.2-18 splines_4.0.5 polyclip_1.10-0
[16] jsonlite_1.8.0 ica_1.0-3 cluster_2.1.3 png_0.1-7 rgeos_0.5-9
[21] uwot_0.1.14 shiny_1.7.2 sctransform_0.3.4 spatstat.sparse_2.1-1 compiler_4.0.5
[26] httr_1.4.4 assertthat_0.2.1 Matrix_1.4-1 fastmap_1.1.0 lazyeval_0.2.2
[31] cli_3.4.1 later_1.2.0 htmltools_0.5.3 tools_4.0.5 igraph_1.3.4
[36] gtable_0.3.1 glue_1.6.2 RANN_2.6.1 reshape2_1.4.4 dplyr_1.0.10
[41] Rcpp_1.0.9 scattermore_0.8 vctrs_0.4.1 nlme_3.1-159 progressr_0.11.0
[46] lmtest_0.9-40 spatstat.random_2.2-0 stringr_1.4.1 globals_0.16.1 mime_0.12
[51] miniUI_0.1.1.1 lifecycle_1.0.2 irlba_2.3.5 goftest_1.2-3 future_1.28.0
[56] MASS_7.3-58.1 zoo_1.8-11 scales_1.2.1 spatstat.core_2.4-4 promises_1.2.0.1
[61] spatstat.utils_2.3-1 parallel_4.0.5 RColorBrewer_1.1-3 yaml_2.3.5 reticulate_1.28
[66] pbapply_1.5-0 gridExtra_2.3 ggplot2_3.3.6 rpart_4.1.16 stringi_1.7.8
[71] rlang_1.0.6 pkgconfig_2.0.3 matrixStats_0.62.0 lattice_0.20-45 ROCR_1.0-11
[76] purrr_0.3.4 tensor_1.5 patchwork_1.1.2 htmlwidgets_1.5.4 cowplot_1.1.1
[81] bit_4.0.4 tidyselect_1.1.2 parallelly_1.32.1 RcppAnnoy_0.0.19 plyr_1.8.7
[86] magrittr_2.0.3 R6_2.5.1 generics_0.1.3 DBI_1.1.3 pillar_1.8.1
[91] withr_2.5.0 mgcv_1.8-40 fitdistrplus_1.1-8 survival_3.4-0 abind_1.4-5
[96] tibble_3.1.8 future.apply_1.9.1 crayon_1.5.1 hdf5r_1.3.6 KernSmooth_2.23-20
[101] utf8_1.2.2 spatstat.geom_2.4-0 plotly_4.10.0 grid_4.0.5 data.table_1.14.2
[106] digest_0.6.29 xtable_1.8-4 tidyr_1.2.1 httpuv_1.6.6 munsell_0.5.0
[111] viridisLite_0.4.1
