HDF5 Output Errors

[channsoden]

Hello,

This issue is traced back from my original issue posted for Sleuth.

The HDF5 output from Kallisto cannot be read by rhdf5 or Sleuth, although it appears normal to me when reading with h5py.

I am running Kallisto on the Savio cluster at UC Berkeley. OS: Scientific Linux 7.4 (Nitrogen) GCC: 4.8.5

This issue affects Kallisto v.0.43.1 and v.0.44.0. I am using the pre-compiled binary for v.0.44.0, and v.0.43.1 was installed to the cluster by someone else, but looks like it is also the pre-compiled binary.

Dependencies for v.0.44.0:

$ ldd $(which kallisto)  
linux-vdso.so.1 =>  (0x00007ffe07d91000)  
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b9e5b038000)  
librt.so.1 => /lib64/librt.so.1 (0x00002b9e5b255000)  
libdl.so.2 => /lib64/libdl.so.2 (0x00002b9e5b45d000)  
libm.so.6 => /lib64/libm.so.6 (0x00002b9e5b661000)  
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b9e5b964000)  
libc.so.6 => /lib64/libc.so.6 (0x00002b9e5bb7a000)  
/lib64/ld-linux-x86-64.so.2 (0x0000561f4790f000)

I am attempting to read the .h5 files on my local machine using Sleuth installed via Bioconductor. OS: Ubuntu 16.04.4 LTS (Xenial Xerus) R: 3.4.3 Sleuth: 0.29.0 rhdf5: 2.25.3

Here are a few sample results including the reference fasta. kallisto_0.44.0_badh5.zip

Best, Christopher

[Qi-Yang-Bioinfo]

Hi Christopher, I'm having the same issue using kallisto V0.45 on ubuntu18.04 and R3.5.1, H5 files generated by kallisto seems broken while tsv files are fine.

[channsoden]

We dug into this on the Sleuth issue, and eventually passed it on as an issue in rhdf5. My workaround was to create a Sleuth Docker container. See https://github.com/pachterlab/sleuth/issues/175#issuecomment-397451628

[Qi-Yang-Bioinfo]

Thank you for providing a solution. :D