0x55555555
commented
1 year ago Can you confirm the files open as expected and you can view the raw data if you use hdfview or h5py to open the fast5 files (ensuring that ENV var is set when you open the tools!).
Previously, I had been able to successfully run tailfindr, but something got messed up in my environment and I had to start the installation over. Now, tailfindr runs, but the output is "empty." Based on previous posted issues, it would seem like it's an issue of the program not finding the plugin, but I have set the path, so I can't figure out what the issue is.
I'm running tailfindr in a Singularity container. Here's what was installed in the container:
apt install -y git cmake build-essential pkg-config automake libtool-bin gettext unzip
install.packages("devtools")
apt install -y libcurl4-openssl-dev libssl-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev
apt install -y libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
apt install -y libhdf5-dev
apt install -y r-base-dev
wget https://github.com/nanoporetech/vbz_compression/releases/download/v1.0.1/ont-vbz-hdf-plugin_1.0.1-1.focal_amd64.deb dpkg -i ont-vbz-hdf-plugin_1.0.1-1.focal_amd64.deb
Then, in my shell, I set:
export HDF5_PLUGIN_PATH=/usr/local/hdf5/lib/plugin
I get no error messages (except for the "cols is now required when using unnest()") and tailfindr completes the run, but the output is empty. I think it still must be an issue with HDF5 and/or the ONT VBZ plugin, but I'm not sure what to try next after making sure the plugin path is set. I think it's an issue with my VBZ plugin setup (as opposed to tailfindr), so I thought I'd ask here.
I'm running this on Ubuntu 20.04.4 LTS.
Thank you for any help!