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Error: Cannot find feature names in this H5AD file #7

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zhengh42 opened this issue May 27, 2020 · 3 comments
Closed

Error: Cannot find feature names in this H5AD file #7

zhengh42 opened this issue May 27, 2020 · 3 comments

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@zhengh42
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File:

The h5ad file was obtained here: https://covid19.cog.sanger.ac.uk/deprez19_restricted.processed.h5ad

I also tried a few other h5ad files and had the same error.

Command:

Convert("deprez19_restricted.processed.h5ad", dest = "h5seurat", overwrite = TRUE)`

Error message:

Warning: Unknown file type: h5ad
Warning: 'assay' not set, setting to 'RNA'
Creating h5Seurat file for version 3.1.2
Adding X as data
Adding X as counts
Error: Cannot find feature names in this H5AD file

> sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

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

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

other attached packages:
[1] SeuratDisk_0.0.0.9009

loaded via a namespace (and not attached):
[1] httr_1.4.1 tidyr_1.1.0 bit64_0.9-7 hdf5r_1.3.2.9000 jsonlite_1.6.1 viridisLite_0.3.0 splines_3.6.1
[8] leiden_0.3.3 assertthat_0.2.1 ggrepel_0.8.2 globals_0.12.5 pillar_1.4.4 lattice_0.20-41 glue_1.4.1
[15] reticulate_1.15 digest_0.6.25 RColorBrewer_1.1-2 colorspace_1.4-1 cowplot_1.0.0 htmltools_0.4.0 Matrix_1.2-18
[22] plyr_1.8.6 pkgconfig_2.0.3 tsne_0.1-3 listenv_0.8.0 purrr_0.3.4 patchwork_1.0.0 scales_1.1.1
[29] RANN_2.6.1 Rtsne_0.15 tibble_3.0.1 ggplot2_3.3.0 ellipsis_0.3.1 withr_2.2.0 ROCR_1.0-11
[36] pbapply_1.4-2 lazyeval_0.2.2 cli_2.0.2 survival_3.1-12 magrittr_1.5 crayon_1.3.4 future_1.17.0
[43] fansi_0.4.1 nlme_3.1-148 MASS_7.3-51.6 ica_1.0-2 tools_3.6.1 fitdistrplus_1.1-1 data.table_1.12.8
[50] lifecycle_0.2.0 stringr_1.4.0 plotly_4.9.2.1 munsell_0.5.0 cluster_2.1.0 irlba_2.3.3 packrat_0.5.0
[57] compiler_3.6.1 rsvd_1.0.3 rlang_0.4.6 grid_3.6.1 ggridges_0.5.2 rstudioapi_0.11 RcppAnnoy_0.0.16
[64] rappdirs_0.3.1 htmlwidgets_1.5.1 igraph_1.2.5 Seurat_3.1.5 gtable_0.3.0 codetools_0.2-16 reshape2_1.4.4
[71] R6_2.4.1 gridExtra_2.3 zoo_1.8-8 dplyr_0.8.5 bit_1.1-15.2 future.apply_1.5.0 uwot_0.1.8
[78] KernSmooth_2.23-17 ape_5.3 stringi_1.4.6 parallel_3.6.1 Rcpp_1.0.4.6 vctrs_0.3.0 sctransform_0.2.1
[85] png_0.1-7 tidyselect_1.1.0 lmtest_0.9-37
@mojaveazure
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Owner

For this specific H5AD file, it's compressed using the LZF filter. This filter is Python-specific, and cannot easily be used in R. To use this file with Seurat and SeuratDisk, you'll need to read it in Python and save it out using the gzip compression

import anndata
adata = anndata.read("deprez19_restricted.processed.h5ad")
adata.write("deprez19_restricted.processed.gzip.h5ad", compression="gzip")

@errcricket
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Similar to above...

I am trying to open an h5ad file from here: https://covid19.cog.sanger.ac.uk/submissions/release1/Immunodeficiency_Nasal_swabs.h5ad

Following your instructions...

import anndata
adata = anndata.read("deprez19_restricted.processed.h5ad")
adata.write("deprez19_restricted.processed.gzip.h5ad", compression="gzip")

I was able to created a gzipped file, but now when I try to use Read10X_h5, I get the following error:

An object with name X/shape does not exist in this group
Calls: soupify_h5 -> Read10X_h5 -> [[ -> [[.H5File
Execution halted

If I try:

   Convert(filename, dest='h5seurat', overwrite=TRUE)
   seurat_object <- LoadH5Seurat(paste(sample, '.h5seurat', sep=''))

I get this error:

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 raw/X as counts
Adding meta.features from raw/var
R: H5Oint.c:3117: H5O__free: Assertion `oh->mesg[u].dirty == 0' failed.
h5.sh: line 1: 21356 Aborted

Very very stuck, any assistance is greatly appreciated.

@errcricket errcricket mentioned this issue Mar 5, 2021
Open
@mehranf96
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For this specific H5AD file, it's compressed using the LZF filter. This filter is Python-specific, and cannot easily be used in R. To use this file with Seurat and SeuratDisk, you'll need to read it in Python and save it out using the gzip compression

import anndata
adata = anndata.read("deprez19_restricted.processed.h5ad")
adata.write("deprez19_restricted.processed.gzip.h5ad", compression="gzip")

thanks, it worked for me :)

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4 participants
@errcricket @mojaveazure @zhengh42 @mehranf96