kraken2 failing in docker on ubuntu

[Zachary Kurtz]

The example run fails on my Ubuntu machine

nextflow run nf-core/bacass -r 1.1.0 -profile docker --input https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_short.csv --kraken2db ${PWD}/minikraken2 --max_memory 40.GB --max_cpus 10

with

Command exit status:
  2

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  kraken2: database ("../minikraken2") does not contain necessary file taxo.k2d

However, I can use minikraken2 db locally. Docker version 19.03.5, nextflow version is 19.10.0.5170. I'm only seeing this in Ubuntu 18.04: the test runs fine on my macbook.

Any guidance?

[Alexander Peltzer]

Is the file specified by the call (taxo.k2d) present? Not sure what this is... can also run locally with my kraken2db just fine (and already used this for 2 projects...). Should probably investigate a bit further then what causes this...

[Zachary Kurtz]

Could it be a volume mounting issue?

For example, I launched the bacass container with the working directory mounted as a volume and run using a local profile and I don't have any issues running kraken2 (e.g. the necessary files are definitely present):
E.g (no errors here):

## host
docker run --entrypoint /bin/bash -m 40GB -v $PWD:$PWD -w $PWD -ti nfcore/bacass:1.1.0

## container
conda install -c bioconda nextflow
nextflow run nf-core/bacass -r 1.1.0 --input https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_short.csv --kraken2db ${PWD}/minikraken2 --max_memory 40.GB --max_cpus 10

Unfortunately, this means that you might not be able to replicate the issue... but it does at least give me a way of running the pipeline.

[Alexander Peltzer]

Ok this seems to be more of a Docker issue than a pipeline problem - closing for now. If there is something similar coming up too frequently, let me know.