Question

Error in H5Fopen

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Entering edit mode

Yijing • 0

@d0a8eb95

Last seen 13 months ago

Germany

Hello,

I am trying to use 'tximport' to create count matrix for counts produced by kallisto aligner.

After typing this:

txi.kallisto <- tximport(files, type = "kallisto", txOut = TRUE)

I got the error:

Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : 
  HDF5. File accessibility. Unable to open file.

My R version is 4.2.3 so I install the 'Rhdf5lib' by:

BiocManager::install("Rhdf5lib")
library(Rhdf5lib)

I also tried install the 'rhdf5' and it was also the same problem.

I also tried this command Sys.setenv(HDF5_USE_FILE_LOCKING = "FALSE") suggested by Mike but did not solve the problem.

I cannot get the sessionInfo:

> sessionInfo()
Error in x$Priority : $ operator is invalid for atomic vectors
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'rhdf5' is missing or broken

Does anyone know how to solve the problem? Many thanks!

rhdf5 Rhdf5lib kallisto tximport • 1.2k views

ADD COMMENT • link 18 months ago Yijing • 0

score 0 · Answer 1 · 2023-04-28

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 1 day ago

United States

You can avoid using HDF5 by pointing to the .tsv files instead of the .h5 files. I realize this doesn't help with your HDF5 issue, but that's orthogonal to your main goal anyway.

ADD COMMENT • link 18 months ago James W. MacDonald 67k

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Hello James,

thank you for your reply. Actually I also tried using tsv files:

files <- file.path(dir, samples$Out, "abundance.tsv")
txi.kallisto.tsv <- tximport(files, type = "kallisto", tx2gene = tx2gene, ignoreAfterBar = TRUE)

But I still got error:

Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read_tsv
Error in infRepImporter(dirname(files[1])) : 
  reading kallisto results from hdf5 files requires Bioconductor package `rhdf5`

Do you know how to solve this problem?

ADD REPLY • link 18 months ago Yijing • 0