Question: Error in H5Fopen with kallisto .h5 files
gravatar for uso2015
3 months ago by
uso20150 wrote:

I used the kallisto for RNA-seq, then import the result "*.h5" by the tximport tools, but I get the following error: Error in H5Fopen(file, "H5FACCRDONLY", native = native) : HDF5. File accessibilty. Unable to open file.

I am trying to import count data from Kallisto to DESeq2 using the tximport package following the instructions here. there is the same error.


R version 3.5.1 (2018-07-02) Platform: x8664-condacos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /software/anaconda2/lib/R/lib/


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

other attached packages: [1] rhdf5_2.26.2

loaded via a namespace (and not attached): [1] compiler3.5.1 tools3.5.1 Rhdf5lib_1.4.2

rhdf5 tximport kallisto • 146 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by uso20150

This sounds like the issue at reported at and

Are you using R / Bioconductor installed via bioconda? It would be helpful if you could update your question to include the output of the command sessionInfo() so we can see the versions of package that you're using. It's also useful to tag the question with rhdf5 since that's where the error is ultimately coming from, and then the maintainer of that package will be notified when post something.

ADD REPLYlink written 3 months ago by Mike Smith3.8k

yes, I installed R via bioconda. I saw the issues, the reason seems to the Rhdf5lib, but I still don't know how to solve it.

ADD REPLYlink modified 3 months ago • written 3 months ago by uso20150

Does updating to Rhdf5lib 1.4.3 resolve this? That version was created specifically to try and fix problems with the bioconda build system.

Can you also try running the command Sys.setenv(HDF5_USE_FILE_LOCKING = "FALSE") and then re-running whatever command is failing.

If that doesn't work, is it possible for you to share the .h5 file so I can try and dig a bit deeper into the HDF5 error message?

ADD REPLYlink modified 3 months ago • written 3 months ago by Mike Smith3.8k

I have solved the problem by reinstalling Rhdf5lib and rhdf5, thanks.

ADD REPLYlink written 3 months ago by uso20150
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