Error trying to open a loom file that is the output of pySCENIC

[gilhornung]

Hi, I'm trying to open a loom file that is the output of pySCENIC, and I'm getting this error:

> loom <- open_loom("pySCENIC/T.cell.pyscenic.loom", mode = "r")
Error in x$create_attr(which, robj = value) : HDF5-API Errors:
    error #000: ../../../src/H5A.c in H5Acreate2(): line 267: no write intent on file
        class: HDF5
        major: Invalid arguments to routine
        minor: Write failed

[dweemx]

Hi @gilhornung, I cannot reproduce your error unfortunately Could you try to run this command:

loom <- H5File$new("pySCENIC/T.cell.pyscenic.loom", mode = "r")

[gilhornung]

Thank you for the reply, I'm sending a link to the file on dropbox, so you will be able to reproduce the error: https://www.dropbox.com/s/vaqkg2or2k6y2sx/T.cell.pyscenic.loom?dl=0

[dweemx]

Hey @gilhornung,

Running

 loom <- open_loom("pySCENIC/T.cell.pyscenic.loom", mode = "r")

works for me

Which version of SCopeLoomR do you use ?

packageVersion("SCopeLoomR")

[gilhornung]

> packageVersion("SCopeLoomR")
[1] ‘0.9.1’
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pheatmap_1.0.12             BiocParallel_1.22.0         forcats_0.5.0              
 [4] stringr_1.4.0               dplyr_0.8.5                 purrr_0.3.4                
 [7] readr_1.3.1                 tidyr_1.0.3                 tibble_3.0.1               
[10] tidyverse_1.3.0             scran_1.14.6                scater_1.14.6              
[13] ggplot2_3.3.2               SingleCellExperiment_1.8.0  SummarizedExperiment_1.18.1
[16] DelayedArray_0.14.0         matrixStats_0.56.0          Biobase_2.48.0             
[19] GenomicRanges_1.38.0        GenomeInfoDb_1.24.0         IRanges_2.22.1             
[22] S4Vectors_0.26.0            BiocGenerics_0.34.0         SCENIC_1.1.2-2             
[25] SCopeLoomR_0.9.1           

loaded via a namespace (and not attached):
  [1] readxl_1.3.1             backports_1.1.8          plyr_1.8.6               igraph_1.2.5            
  [5] GSEABase_1.50.0          usethis_1.6.1            digest_0.6.25            htmltools_0.5.0         
  [9] viridis_0.5.1            fansi_0.4.1              magrittr_1.5             memoise_1.1.0           
 [13] limma_3.44.1             remotes_2.1.1            annotate_1.66.0          modelr_0.1.7            
 [17] R.utils_2.9.2            prettyunits_1.1.1        colorspace_1.4-1         rvest_0.3.5             
 [21] blob_1.2.1               haven_2.2.0              xfun_0.14                callr_3.4.3             
 [25] crayon_1.3.4             RCurl_1.98-1.2           jsonlite_1.6.1           graph_1.66.0            
 [29] glue_1.4.1               registry_0.5-1           repotools_1.10.1         gtable_0.3.0            
 [33] zlibbioc_1.34.0          XVector_0.28.0           pkgbuild_1.0.8           BiocSingular_1.2.2      
 [37] scales_1.1.1             DBI_1.1.0                edgeR_3.30.0             bibtex_0.4.2.2          
 [41] Rcpp_1.0.4.6             viridisLite_0.3.0        xtable_1.8-4             dqrng_0.2.1             
 [45] bit_1.1-15.2             rsvd_1.0.3               httr_1.4.1.9000          RColorBrewer_1.1-2      
 [49] ellipsis_0.3.1           pkgconfig_2.0.3          XML_3.99-0.3             R.methodsS3_1.8.0       
 [53] dbplyr_1.4.3             locfit_1.5-9.4           tidyselect_1.1.0         rlang_0.4.6             
 [57] later_1.1.0.1            AnnotationDbi_1.50.0     munsell_0.5.0            cellranger_1.1.0        
 [61] tools_3.6.3              cli_2.0.2                generics_0.0.2           RSQLite_2.2.0           
 [65] devtools_2.3.0           broom_0.5.6              fastmap_1.0.1            processx_3.4.2          
 [69] knitr_1.28               bit64_0.9-7              fs_1.4.1                 nlme_3.1-147            
 [73] mime_0.9                 R.oo_1.23.0              xml2_1.3.2               hdf5r_1.3.2.9000        
 [77] compiler_3.6.3           rstudioapi_0.11          beeswarm_0.2.3           curl_4.3                
 [81] testthat_2.3.2           reprex_0.3.0             rversions_2.0.1          statmod_1.4.34          
 [85] stringi_1.4.6            ps_1.3.3                 desc_1.2.0               lattice_0.20-41         
 [89] Matrix_1.2-18            vctrs_0.3.1              pillar_1.4.4             lifecycle_0.2.0         
 [93] BiocNeighbors_1.4.2      data.table_1.12.8        bitops_1.0-6             irlba_2.3.3             
 [97] httpuv_1.5.4             AUCell_1.8.0             R6_2.4.1                 promises_1.1.1          
[101] gridExtra_2.3            vipor_0.4.5              sessioninfo_1.1.1        codetools_0.2-16        
[105] assertthat_0.2.1         pkgload_1.1.0            pkgmaker_0.31.2          rprojroot_1.3-2         
[109] withr_2.2.0              GenomeInfoDbData_1.2.3   hms_0.5.3                grid_3.6.3              
[113] DelayedMatrixStats_1.8.0 shiny_1.4.0.2            lubridate_1.7.8          ggbeeswarm_0.6.0

[gilhornung]

I am able to open the file with the LoomExperiment package

[dweemx]

Very weird... I even updated the hdf5r package to match your version but it still works for me

[gilhornung]

I found a workaround. I load the loom file using the LoomExperiment package, and use the AUC data that is found in the colData slot. I'm placing the code here in case someone lands on this page. Would also appreciate it if you could tell me if the way I pull the AUC data is valid:

  library(LoomExperiment)

  df <- colData(import(loomfile))
  regulon_colnames <- grep("RegulonsAUC",colnames(df), value = T) 
  regulons <- stringr::str_match(regulon_colnames,
                                 pattern = "RegulonsAUC[.](.*?)[.][.][.]")[,2]
  mat <- t(as.matrix(df[,regulon_colnames]))
  colnames(mat) <- df$CellID
  rownames(mat) <- regulons

[dweemx]

Yes, this should work. I see quite a lot of warnings() do also have these when importing the Loom ?

[dweemx]

Closing issue since no activity Please reopen issue if still encountering this issue