Daniel Donovan

I prefer it the way it is b/c I setup my dockerfile as: ``` FROM ubuntu:20.04 ARG DEBIAN_FRONTEND=noninteractive ARG VERSION=0.22.0 # Application installation RUN wget -O fastp http://opengene.org/fastp/fastp.${VERSION} && \...

I can just create a `Blueprint` for `/api/search/cli`; I don't need to hook into the `Namespace` object.

Here is the contents of `pplacer out` ``` Running pplacer v1.1.alpha19-0-g807f6f3 analysis on checkm_folder/storage/tree/concatenated.fasta... Didn't find any reference sequences in given alignment file. Using supplied reference alignment. Pre-masking sequences... sequence...

I'm not sure if this is relavent https://github.com/Ecogenomics/GTDBTk/issues/170#issuecomment-514466145

Update: I am able to run `pplacer` independently of checkm after it fails. Here are the steps I took: - Run `checkm` until where it fails - cd into `checkm_folder/storage/tree`...

I am also seeing this behavior with the `nextflow` engine as well.