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I've been using tximport with output from Kallisto. After recent updates, including R to 3.6.1, I now get the following error on Windows:
txi.kallisto=tximport(files,type="kallisto",txOut=T,ignoreTxVersion = T,countsFromAbundance = 'scaledTPM')
Error in rhdf5::h5ls(h5File) : HDF5. Object header. Can't open object.
Using R 3.6.1 in Linux I'm able to import without error from the same abundance.h5 files without an error.
If I try to diagnose the problem with h5read, I get this error:
k=rhdf5::h5read("results/S1/abundance.h5")
Error in H5Lexists(loc$H5Identifier, name) :
argument "name" is missing, with no default
Any idea why tximport gives an error?
Here's the sessionInfo()
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tximport_1.12.3 rhdf5_2.28.0
loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1 Rhdf5lib_1.6.0
Your call to
rhdf5::h5read()needs to you to specify the name of the dataset to extract via thenameargument. That's the source of the error your getting there.To try and recreate the tximport usage you want to try
rhdf5::h5ls()which will grab the entire contents of the file.Thanks. h5lc() showed the contents of the file correctly.
Working backwards from that I am now able to import on Windows without error. Don't know what changed or if there was an error in my files vector.
In any case, problem solved and sorry to waste your time.