Have some issues in running prokka on WSL

Question

[Kirill]

Hello!

I'm trying to run prokka with standard parameters

prokka --force genome.fasta

And then getting this error:

[01:21:21] Looking for 'blastp' - found /home/matikmate/miniconda3/envs/prokka/bin/blastp                                                                blastp: symbol lookup error: /home/matikmate/miniconda3/envs/prokka/bin/../lib/ncbi-blast+/./libxcompress.so: undefined symbol: ZSTD_DCtx_loadDictionary  
[01:21:21] Could not determine version of blastp - please install version 2.8 or higher

Tried to update BLAST, but package is already installed. Also can't run blastp/blastn itself, getting same error.

Thanks in advance!

Answer 1

[Philipp Bayer]

It looks like the conda-installed BLAST has issues with the system's ZSTD, which is probably some WSL weirdness. You might be able to fix it up by upgrading WSL, see here.

You can also get around this by running the prokka Docker container, see here on how to install Docker under WSL, then install the Docker container, from the prokka manual:

docker pull staphb/prokka:latest
docker run staphb/prokka:latest prokka -h

[Kirill]

Thank you for the answer!

As it turned out i just needed to install ZSTD package into the environment :)

[Philipp Bayer]

great to hear! That should've been installed by the conda recipe, I have a hunch these aren't tested too well with WSL.