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)
--
You received this message because you are subscribed to the Google Groups "kallisto and applications" group.
To unsubscribe from this group and stop receiving emails from it, send an email to kallisto-and-appli...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/kallisto-and-applications/a1ecc1a5-7ad8-4c87-b6d2-f7f3b6a3b60cn%40googlegroups.com.