HDF5-API Error when attempting to connect to loom file

[davisidarta]

Hello everyone

I'm trying to connect to a loom file in order to extract counts for further analysis. However, when I run connect(), I get the following error output:

> lfile <- connect(filename = "l1_hypothalamus.loom", mode = "r+")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: ../../../src/H5F.c in H5Fopen(): line 579: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: ../../../src/H5Fint.c in H5F_open(): line 1100: unable to open file: time = Thu Apr 25 04:42:56 2019
, name = '/home/rstudio/analysis/linnarson/l1_hypothalamus.loom', tent_flags = 1
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #002: ../../../src/H5FD.c in H5FD_open(): line 812: open failed
        class: HDF5
        major: Virtual File Layer
        minor: Unable to initialize object

    error #003: ../../../src/H5FDsec2.c in H5FD_sec2_open(): line 348: unable to open file: name = '/home/rstudio/analysis/linnarson/l1_hypothalamus.loom', errno = 13, error message = 'Permission denied', flags = 1, o_flags = 2
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

I have already installed and reinstalled hdf5, both in the rocker/tidyverse docker image in which I'm running RStudio and in our local cluster operating system (I'm running a Ubuntu 18.10.04 LTS). I've never had this error before.

Any insights on what this could be?

[mojaveazure]

From error 003 in the output:

error message = 'Permission denied'

Check to ensure you have read and write permissions (since you're opening in r+ mode) to the loom file.

[bellenger-l]

Hello

I have quite the same issue while running the create function of loomR :

loomR::create("file.loom",
       data = as.matrix(raw_expression_matrix),
       cell.attrs = transcriptome_metadata,
       gene.attrs = NULL,
       do.transpose = TRUE, overwrite = TRUE)

But I don't really understand your reply

Check to ensure you have read and write permissions (since you're opening in r+ mode) to the loom file.

I think I cannot apply to my case. Here is the complete error message :

Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: ../../../src/H5F.c in H5Fcreate(): line 522: unable to create file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: ../../../src/H5Fint.c in H5F_open(): line 1024: unable to truncate a file which is already open
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

Can you help me please ?

Best, Lea