Closed kleurless closed 4 years ago
Thanks for reposting with a clear example. We're working on this now.
Hi, I am also getting the same error as above. Thanks for looking into this.
scanpy environment
scanpy==1.4.6 anndata==0.7.1 umap==0.3.10 numpy==1.18.1 scipy==1.4.1 pandas==1.0.1 scikit-learn==0.22.1 statsmodels==0.11.0 python-igraph==0.7.1 louvain==0.6.1
Seurat environment
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (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/3.6/Resources/lib/libRlapack.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] Seurat_3.1.4
loaded via a namespace (and not attached):
[1] tsne_0.1-3 nlme_3.1-145 bitops_1.0-6 bit64_0.9-7 RcppAnnoy_0.0.16
[6] RColorBrewer_1.1-2 httr_1.4.1 numDeriv_2016.8-1.1 sctransform_0.2.1 tools_3.6.0
[11] R6_2.4.1 irlba_2.3.3 KernSmooth_2.23-16 uwot_0.1.8 lazyeval_0.2.2
[16] BiocGenerics_0.32.0 colorspace_1.4-1 sn_1.6-0 npsurv_0.4-0 gridExtra_2.3
[21] tidyselect_1.0.0 mnormt_1.5-6 bit_1.1-15.2 compiler_3.6.0 cli_2.0.2
[26] Biobase_2.46.0 hdf5r_1.3.2 TFisher_0.2.0 plotly_4.9.2 sandwich_2.5-1
[31] caTools_1.18.0 scales_1.1.0 lmtest_0.9-37 mvtnorm_1.1-0 ggridges_0.5.2
[36] pbapply_1.4-2 rappdirs_0.3.1 stringr_1.4.0 digest_0.6.25 htmltools_0.4.0
[41] pkgconfig_2.0.3 bibtex_0.4.2.2 plotrix_3.7-7 htmlwidgets_1.5.1 rlang_0.4.5
[46] rstudioapi_0.11 zoo_1.8-7 jsonlite_1.6.1 ica_1.0-2 gtools_3.8.2
[51] dplyr_0.8.5 magrittr_1.5 patchwork_1.0.0.9000 Matrix_1.2-18 Rcpp_1.0.4
[56] munsell_0.5.0 fansi_0.4.1 ape_5.3 reticulate_1.14 lifecycle_0.2.0
[61] stringi_1.4.6 multcomp_1.4-12 gbRd_0.4-11 MASS_7.3-51.5 gplots_3.0.3
[66] Rtsne_0.15 plyr_1.8.6 grid_3.6.0 parallel_3.6.0 gdata_2.18.0
[71] listenv_0.8.0 ggrepel_0.8.2 crayon_1.3.4 lattice_0.20-40 cowplot_1.0.0
[76] splines_3.6.0 multtest_2.42.0 pillar_1.4.3 igraph_1.2.5 reshape2_1.4.3
[81] future.apply_1.4.0 codetools_0.2-16 stats4_3.6.0 leiden_0.3.3 mutoss_0.1-12
[86] glue_1.3.2 lsei_1.2-0 metap_1.3 data.table_1.12.8 png_0.1-7
[91] vctrs_0.2.4 Rdpack_0.11-1 tidyr_1.0.2 gtable_0.3.0 RANN_2.6.1
[96] purrr_0.3.3 future_1.16.0 assertthat_0.2.1 ggplot2_3.3.0 rsvd_1.0.3
[101] viridisLite_0.3.0 survival_3.1-11 tibble_3.0.0 cluster_2.1.0 globals_0.12.5
[106] fitdistrplus_1.0-14 TH.data_1.0-10 ellipsis_0.3.0 ROCR_1.0-7
I have a similar probleem:
I am trying to read a .h5ad file using the function> file.seurat <- ReadH5AD(file = "D:/.../file.h5ad")
I am getting the following error:
Pulling expression matrices and metadata Error in self$read_low_level(file_space = self_space_id, mem_space = mem_space_id, : HDF5-API Errors: error #000: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dio.c in H5Dread(): line 173: can't read data class: HDF5 major: Dataset minor: Read failed
error #001: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dio.c in H5D__read(): line 551: can't read data class: HDF5 major: Dataset minor: Read failed
error #002: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_read(): line 1875: unable to read raw data chunk class: HDF5 major: Low-level I/O minor: Read failed
error #003: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_lock(): line 2905: data pipeline read failed class: HDF5 major: Data filters minor: Filter operation failed
error #004: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Z.c in H5Z_pipeline(): line 1347: required filter 'lzf' is not registered class: HDF5 major: Data filters minor: Read failed
Hi,
We are transitioning our support for AnnData/H5AD files to SeuratDisk, our new package for interfacing Seurat
objects with single-cell HDF5-based file formats. We would very much like it if you could give this a shot for reading in your data.
You can install SeuratDisk with the following:
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github("mojaveazure/seurat-disk")
A tutorial on how to read in AnnData/H5AD files via the h5Seurat intermediate can be found here. Greater detail about the new Convert
mechanism can be found here
If you come across any bugs in reading in your HDF5 files, please post them in mojaveazure/seurat-disk#1. Please note, there are some stipulations about the format of your AnnData/H5AD posted in https://github.com/mojaveazure/seurat-disk/issues/1#issue-619215532
@mojaveazure Thanks alot for your help. Will check it out.
Hi,
We are transitioning our support for AnnData/H5AD files to SeuratDisk, our new package for interfacing
Seurat
objects with single-cell HDF5-based file formats. We would very much like it if you could give this a shot for reading in your data.You can install SeuratDisk with the following:
if (!requireNamespace("remotes", quietly = TRUE)) { install.packages("remotes") } remotes::install_github("mojaveazure/seurat-disk")
A tutorial on how to read in AnnData/H5AD files via the h5Seurat intermediate can be found here. Greater detail about the new
Convert
mechanism can be found hereIf you come across any bugs in reading in your HDF5 files, please post them in mojaveazure/seurat-disk#1. Please note, there are some stipulations about the format of your AnnData/H5AD posted in mojaveazure/seurat-disk#1 (comment)
It worked for me. Thanks a lot!
SeuratDisk approach works for me as well:
eg from AnnData to Seurat object
Convert("scanpy_object.h5ad", dest = "h5seurat", overwrite = F)
scanpy_object_Seurat <- LoadH5Seurat("scanpy_object.h5seurat")
scanpy=1.5.1 anndata=0.7.3 h5py=2.10.0 hdf5=1.10.6
@mojaveazure Thank a lot for solving this!
Hi!
I mainly analyse my data using SCANPY, but I want to try out CCA batch correction. I have a few .h5ad files with some of my datasets. But everytime I try to read them in Seurat using the function:
data <- ReadH5AD("~/file_name.h5ad", assay="RNA")
I get the following error:Here is a dataset that throws this error: https://drive.google.com/file/d/1QnH7FiyIIX1GDaKR1fQC5qsE5coT-hIc/view?usp=sharing
Below are my scanpy versions:
scanpy==1.4.5.1 anndata==0.7.1 umap==0.3.10 numpy==1.18.1 scipy==1.4.1 pandas==1.0.1 scikit-learn==0.21.3 statsmodels==0.11.0 python-igraph==0.7.1+4.bed07760 louvain==0.6.1 scvelo==0.1.26.dev22+gf165453 loompy==3.0.6 matplotlib==3.1.3
And this is the output of
sessionInfo()
:And yes, this is the exact same issue as #2485, but that one is closed due to not enough information.