Entering edit mode
20 months ago
c2e09af0
•
0
Dear everyone,
I'm new to bioinformatics and need to reduce two scRNAseq-Seurat objects to their shared genes and convert the files to the h5ad format for further analysis.
My approach is:
SaveH5Seurat(dat5, filename = "data.h5Seurat")
Convert("data.h5Seurat", dest = "h5ad")
Since the code worked fine for one of the two files I have no clue what the problem is. The second (already pre-processed) exprMatrix.tsv.gz originates from here: https://cells-test.gi.ucsc.edu/?ds=early-brain The Convert()-command is producing an error for the second file. The error message is:
Validating h5Seurat file Adding data from RNA as X Adding counts from
RNA as raw Transfering meta.data to obs Error in self$flush() :
HDF5-API Errors:
error #000: H5F.c in H5Fflush(): line 677: unable to flush file
class: HDF5
major: File accessibility
minor: Unable to flush data from cache
error #001: H5VLcallback.c in H5VL_file_specific(): line 3769: file specific failed
class: HDF5
major: Virtual Object Layer
minor: Can't operate on object
error #002: H5VLcallback.c in H5VL__file_specific(): line 3699: file specific failed
class: HDF5
major: Virtual Object Layer
minor: Can't operate on object
error #003: H5VLnative_file.c in H5VL__native_file_specific(): line 316: unable to flush mounted file hierarchy
class: HDF5
major: File accessibility
minor: Unable to flush data from cache
error #004: H5Fmount.c in H5F_flush_mounts(): line 692: unable to flush mounted file hierarchy
class: HDF5
major: File accessibility
minor: Unable to flush data from cache
error #005:
Thank you so much in advance for any kind of help!
Also, here's my session info:
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /home/rstudio-server/.conda/envs/r4/lib/libopenblasp-r0.3.18.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.1.1 scater_1.22.0 ggplot2_3.3.6 scuttle_1.4.0
[5] SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1
[9] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 BiocGenerics_0.40.0
[13] MatrixGenerics_1.6.0 matrixStats_0.62.0 data.table_1.14.2 sp_1.5-0
[17] SeuratObject_4.1.0 Seurat_4.1.1 SeuratData_0.2.2 SeuratDisk_0.0.0.9020
loaded via a namespace (and not attached):
[1] plyr_1.8.7 igraph_1.3.4 lazyeval_0.2.2 splines_4.1.2
[5] BiocParallel_1.28.3 listenv_0.8.0 scattermore_0.8 digest_0.6.29
[9] htmltools_0.5.3 viridis_0.6.2 fansi_1.0.3 magrittr_2.0.3
[13] ScaledMatrix_1.2.0 tensor_1.5 cluster_2.1.2 ROCR_1.0-11
[17] globals_0.16.0 spatstat.sparse_2.1-1 colorspace_2.0-3 rappdirs_0.3.3
[21] ggrepel_0.9.1 dplyr_1.0.9 crayon_1.5.1 RCurl_1.98-1.8
[25] jsonlite_1.8.0 progressr_0.10.1 spatstat.data_2.2-0 survival_3.2-13
[29] zoo_1.8-10 glue_1.6.2 polyclip_1.10-0 gtable_0.3.0
[33] zlibbioc_1.40.0 XVector_0.34.0 leiden_0.4.2 DelayedArray_0.20.0
[37] BiocSingular_1.10.0 future.apply_1.9.0 abind_1.4-5 scales_1.2.0
[41] spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.9 viridisLite_0.4.0
[45] xtable_1.8-4 reticulate_1.25 spatstat.core_2.4-4 bit_4.0.4
[49] rsvd_1.0.5 htmlwidgets_1.5.4 httr_1.4.3 RColorBrewer_1.1-3
[53] ellipsis_0.3.2 ica_1.0-3 pkgconfig_2.0.3 uwot_0.1.11
[57] deldir_1.0-6 utf8_1.2.2 tidyselect_1.1.2 rlang_1.0.4
[61] reshape2_1.4.4 later_1.3.0 munsell_0.5.0 tools_4.1.2
[65] cli_3.3.0 generics_0.1.3 ggridges_0.5.3 stringr_1.4.0
[69] fastmap_1.1.0 goftest_1.2-3 bit64_4.0.5 fitdistrplus_1.1-8
[73] purrr_0.3.4 RANN_2.6.1 pbapply_1.5-0 future_1.27.0
[77] nlme_3.1-155 sparseMatrixStats_1.6.0 mime_0.12 hdf5r_1.3.5
[81] compiler_4.1.2 rstudioapi_0.13 beeswarm_0.4.0 plotly_4.10.0
[85] png_0.1-7 spatstat.utils_2.3-1 tibble_3.1.8 stringi_1.7.8
[89] rgeos_0.5-9 lattice_0.20-45 Matrix_1.4-0 vctrs_0.4.1
[93] pillar_1.8.0 lifecycle_1.0.1 spatstat.geom_2.4-0 lmtest_0.9-40
[97] RcppAnnoy_0.0.19 BiocNeighbors_1.12.0 cowplot_1.1.1 bitops_1.0-7
[101] irlba_2.3.5 httpuv_1.6.5 R6_2.5.1 promises_1.2.0.1
[105] KernSmooth_2.23-20 gridExtra_2.3 vipor_0.4.5 parallelly_1.32.1
[109] codetools_0.2-18 MASS_7.3-55 withr_2.5.0 sctransform_0.3.3
[113] GenomeInfoDbData_1.2.7 mgcv_1.8-38 parallel_4.1.2 grid_4.1.2
[117] rpart_4.1.16 beachmat_2.10.0 tidyr_1.2.0 DelayedMatrixStats_1.16.0
[121] Rtsne_0.16 shiny_1.7.2 ggbeeswarm_0.6.0
