Unable to read HDF5 biom file

[chlige]

I am trying to read in a BIOM v2 file (HDF5) using the read_biom function and receive the following error message. I would think the try statements in read_biom would work and properly open the file. Perhaps there is a change in R v4.3.0?

> genus_biom <- read_biom("metagenomics/genus_summary_clean/feature-table.biom")
Warning messages:
1: In strsplit(conditionMessage(e), "\n") :
  unable to translate 'lexical error: invalid char in json text.
                                       <89>HDF  �                      (right here) ------^
' to a wide string
2: In strsplit(conditionMessage(e), "\n") : input string 1 is invalid

I am able to open the file using the following command.

genus_biom <- biom(read_hdf5_biom("genus_summary_clean/feature-table.biom"))

Here are details for my installation of R and biomformat.

> installed.packages()["biomformat", "Version"]
[1] "1.28.0"
> version
               _                                
platform       x86_64-w64-mingw32               
arch           x86_64                           
os             mingw32                          
crt            ucrt                             
system         x86_64, mingw32                  
status                                          
major          4                                
minor          3.0                              
year           2023                             
month          04                               
day            21                               
svn rev        84292                            
language       R                                
version.string R version 4.3.0 (2023-04-21 ucrt)
nickname       Already Tomorrow                 

> read_biom
function (biom_file) 
{
    trash = try(silent = TRUE, expr = {
        x <- fromJSON(biom_file, simplifyDataFrame = FALSE, simplifyMatrix = FALSE)
    })
    if (inherits(trash, "try-error")) {
        trash = try(silent = TRUE, expr = {
            x <- read_hdf5_biom(biom_file)
        })
    }
    if (inherits(trash, "try-error")) {
        stop("Both attempts to read input file:\n", biom_file, 
            "\n", "either as JSON (BIOM-v1) or HDF5 (BIOM-v2).\n", 
            "Check file path, file name, file itself, then try again.")
    }
    return(biom(x))
}
<bytecode: 0x000001a1c3204da8>
<environment: namespace:biomformat>
>

Any help in this matter would be greatly appreciated.

Thanks!

• George

[svillegasv]

I was experiencing the same problem. What seemed to work was to convert the .biom from hdf5 to json in the command line using:

biom convert -i input_hdf5_file.biom -o output_json_file.biom --to-json

Later, I was able to load the resulting biom file into R using the read_biom2phyloseq function from the microbiome package and add the metadata as an argument in the same function.

Hope it helps.