no HDF5 files created after compiling, sleuth won't read .tsv

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Schaler Starks

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Jun 5, 2023, 3:55:44 PM6/5/23
to kallisto and applications

kallisto/build % cmake .. -DUSE_HDF5=ON             

shared build

-- Configuring done (3.0s)

-- Generating done (0.1s)

-- Build files have been written to: /usr/local/Cellar/kallisto


Running kallisto, however told me that HDF5 support was not available:

[quant] fragment length distribution will be estimated from the data

Warning: kallisto was not compiled with HDF5 support so no bootstrapping

will be performed. Run quant with --plaintext option or recompile with

HDF5 support to obtain bootstrap estimates.

------------------------------------------------------------------------------------------------------------------------

I was able to get `abundance.tsv` files for all of my samples, but running gave:

> so <- sleuth_prep(s2c, extra_bootstrap_summary = TRUE)

reading in kallisto results

dropping unused factor levels

.............................................normalizing est_counts

47141 targets passed the filter

normalizing tpm

merging in metadata

Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : 

  HDF5. File accessibilty. Unable to open file.


For reference, I am referring to Getting Started with sleuth. As far as I am aware from the Github releases, shouldn't sleuth work in conjunction with abundance.tsv files? If not, then what else should I try to compile with HDF5 on?

(Possibly relevant: MacOS, Intel, sleuth in R, kallisto compiled from scratch using Homebrew)

Pall Melsted

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Jun 6, 2023, 6:28:53 AM6/6/23
to kallisto and applications
When  you build kallisto with hdf5 it should output hd5 files.

If all else fails, the binary builds are build using this option so you can download them from the release page on github, https://github.com/pachterlab/kallisto/releases

When you run the cmake command, does it specify that it found the HDF5 libraries?

Are you running kallisto with a full path or the installed version? What happens when you run

which kallisto

it might be pointing to an older version. 

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